website/2dbase-ecoli.html 0000644 0002441 0001757 00000007466 11606605735 015457 0 ustar jison industry
Bioinformatics Data Resource Catalogue
2D-PAGE database of Escherichia coli
This Database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins where identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analysed and compared in a tabular format based on varios functional categories enabling quick and subsequent analysis.
Available data
Example queries
website/2dpage.html 0000644 0002441 0001757 00000003037 11606605726 014356 0 ustar jison industry
Bioinformatics Data Resource Catalogue
2D-PAGE proteome database system for microbial research
Two-dimensional gel electrophoresis (2-DE) and mass spectrometry data of diverse microorganisms and other organisms.
website/3dgenomics.html 0000644 0002441 0001757 00000002746 11606605726 015255 0 ustar jison industry
Bioinformatics Data Resource Catalogue
3D-Genomics database of structural annotations for proteomes
Structural annotations for the proteomes of just under 100 organisms. Using data derived from public databases of translated genomic sequences, representatives from the major branches of Life are included: Prokaryota, Eukaryota and Archaea.
website/3did.html 0000644 0002441 0001757 00000022356 11606605726 014044 0 ustar jison industry
Bioinformatics Data Resource Catalogue
3DID database of 3D interacting domains
A collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known.
Available data
Example queries
website/3dmet.html 0000644 0002441 0001757 00000002602 11606605726 014225 0 ustar jison industry
Bioinformatics Data Resource Catalogue
3DMET
Three-dimensional structures of natural metabolites.
website/4dxpress.html 0000644 0002441 0001757 00000005617 11606605726 014776 0 ustar jison industry
Bioinformatics Data Resource Catalogue
4DXpress cross species gene expression pattern database
A platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments.
Available data
Example queries
website/5srrna.html 0000644 0002441 0001757 00000002651 11606605726 014427 0 ustar jison industry
Bioinformatics Data Resource Catalogue
5S rRNA database
Information on nucleotide sequences of 5S rRNAs and their genes.
website/a1atvar.html 0000644 0002441 0001757 00000002454 11606605726 014555 0 ustar jison industry
Bioinformatics Data Resource Catalogue
A1ATVar A1-antitrypsin database
Database of human SERPINA1 gene variants leading to alpha1-antitrypsin deficiency
website/aarhus_ghent-2dpage.html 0000644 0002441 0001757 00000003071 11606605726 017022 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Aarhus_Ghent-2DPAGE
Human keratinocyte 2D gel protein database from Aarhus and Ghent universities
Human keratinocyte 2D gel protein database from Aarhus and Ghent universities
Example queries
| Data |
Format |
Query |
Example |
website/abcdb.html 0000644 0002441 0001757 00000002532 11606605726 014246 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Archaeal and bacterial ABC transporter database (ABCdb)
Archaeal and bacterial ABC transporter database.
website/abs.html 0000644 0002441 0001757 00000005523 11606605726 013763 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ABS database of binding sites from orthologous promoters
Annotated regulatory binding sites from orthologous promoters.
Available data
Example queries
website/aceview.html 0000644 0002441 0001757 00000020206 11606605726 014634 0 ustar jison industry
Bioinformatics Data Resource Catalogue
AceView genes database
A curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace).
Available data
Example queries
| Data |
Format |
Query |
Example |
website/aclame.html 0000644 0002441 0001757 00000002527 11606605726 014441 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ACLAME classification of mobile genetic elements
Collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.
website/affindb.html 0000644 0002441 0001757 00000002431 11606605726 014602 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Affinity database (AffinDB) for protein–ligand complexes
Affinity database for protein–ligand complexes
website/aftol.html 0000644 0002441 0001757 00000005544 11606605726 014326 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Assembling the Fungal Tree of Life (AFTOL) database
Fungal structural and biochemical database.
Available data
Example queries
| Data |
Format |
Query |
Example |
website/agd.html 0000644 0002441 0001757 00000026155 11606605726 013755 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ashbya genome database (AGD)
A genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from Ashbya gossypii and the model organism Saccharomyces cerevisiae. It also provides access to comparative genomics data from those two fungi as well as Schizosaccharomyces pombe and Neurospora crassa.
Available data
Example queries
website/allergome.html 0000644 0002441 0001757 00000005457 11606605727 015174 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Allergome; a platform for allergen knowledge
Allergome; a platform for allergen knowledge
Available data
Example queries
website/amypdb.html 0000644 0002441 0001757 00000002425 11606605727 014471 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Amyloid precursor proteins database (AMYPDB)
Amyloid precursor families and their amino acid sequence signatures.
website/anpr.html 0000644 0002441 0001757 00000003275 11606605727 014161 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Arabidopsis nucleolar protein database (ANPR)
Comparative analysis of human and Arabidopsis nucleolar proteomes
website/antibodypedia.html 0000644 0002441 0001757 00000002532 11606605727 016030 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Antibodypedia database of antibodies to human proteins
Application-specific validation of publicly available antibodies to human protein targets.
website/antijen.html 0000644 0002441 0001757 00000003562 11606605727 014650 0 ustar jison industry
Bioinformatics Data Resource Catalogue
AntiJen database for peptides binding to immunity related proteins
Quantitative binding data for peptides binding to MHC Ligand, TCR-MHC Complexes, T Cell Epitope, TAP, B Cell Epitope molecules and immunological protein-protein interactions. AntiJen includes Peptide Library, Copy Numbers and Diffusion Coefficient data.
website/anu-2dpage.html 0000644 0002441 0001757 00000006417 11606605727 015145 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Australian National University 2-DE database (ANU-2DPAGE)
2-DE PAGE database.
Available data
Example queries
website/aphidbase.html 0000644 0002441 0001757 00000002620 11606605727 015132 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Aphid genome database (AphidBase)
Aphid genome database
website/apidb_cryptodb.html 0000644 0002441 0001757 00000006272 11606605727 016206 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Cryptosporidium genome resources (CryptoDB)
Genomic-scale dataset associated with the eukaryotic pathogens Cryptosporidium.
Available data
Example queries
website/apidb_giardiadb.html 0000644 0002441 0001757 00000006260 11606605727 016263 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Giardia genome resources (GiardiaDB)
Genomic-scale datasets for the eukaryotic pathogen Giardia.
Available data
Example queries
website/apidb_plasmodb.html 0000644 0002441 0001757 00000006251 11606605727 016156 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Plasmodium genome resources (PlasmoDB)
Genomic-scale dataset associated with the eukaryotic pathogens Plasmodium.
Available data
Example queries
website/apidb_toxodb.html 0000644 0002441 0001757 00000006222 11606605727 015652 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Toxoplasma genome resources (ToxoDB)
Genomic-scale datasets associated with the eukaryotic pathogens Toxoplasma.
Available data
Example queries
website/apidb_trichdb.html 0000644 0002441 0001757 00000006241 11606605727 015773 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Trichomonas genome resources (TrichDB)
Genomic-scale datasets associated with the eukaryotic Trichomonas.
Available data
Example queries
website/apidb_tritrypdb.html 0000644 0002441 0001757 00000006233 11606605727 016400 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Kinetoplastid genome resources (TritryPDB)
Kinetoplastid genome resources.
Available data
Example queries
website/apid.html 0000644 0002441 0001757 00000002660 11606605727 014133 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Agile protein interaction data analyzer (APID)
Integrated database of protein-protein interactions providing access to all known experimentally validated protein-protein interactions (BIND, BioGRID, DIP, HPRD, IntAct and MINT).
website/appadb.html 0000644 0002441 0001757 00000003515 11606605727 014445 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Pristionchus.org P. pacificus database (AppaDB)
Genomic data of P.pacificus, including the physical map, genetic linkage map, EST and BAC end sequence and hybridization data.
website/arachnoserver.html 0000644 0002441 0001757 00000005605 11606605727 016062 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ArachnoServer
Spider toxin database
Available data
Example queries
website/arac-xyls.html 0000644 0002441 0001757 00000006404 11606605727 015121 0 ustar jison industry
Bioinformatics Data Resource Catalogue
AraC-XylS database of a family of Helix-Turn-Helix transcription factors from bacteria
A database on a family of Helix-Turn-Helix transcription factors from bacteria.
Available data
Example queries
website/aramemnon.html 0000644 0002441 0001757 00000005520 11606605727 015171 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ARAMEMNON database of plant membrane proteins
Plant membrane proteins.
Available data
Example queries
website/archdb.html 0000644 0002441 0001757 00000005320 11606605727 014435 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ArchDB database of loop structures
ArchDB database of loop structures.
Available data
Example queries
website/argonaute.html 0000644 0002441 0001757 00000004070 11606605727 015200 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Argonaute database of mammalian microRNAs regulatory function
A database on mammalian miRNAs and their known or predicted regulatory targets. It provides information on origin of miRNAs, tissue specificity of their expressions and their known or proposed functions, their potential target genes as well as data on miRNA families based on their coexpression and proteins known to be involved in miRNA processing.
website/arrayexpress.html 0000644 0002441 0001757 00000010717 11606605727 015750 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ArrayExpress repository for microarray data
A public archive for functional genomics data compliant with MIAME- and MINSEQE requirements in accordance with compliant data in accordance with MGED recommendations. Includes gene-indexed expression profiles.
Available data
Example queries
website/asap.html 0000644 0002441 0001757 00000003450 11606605730 014132 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Systematic annotation package for community analysis of genomes (ASAP)
Genome sequences, associated annotations and functional characterization data for E. coli K-12.
Example queries
| Data |
Format |
Query |
Example |
website/asc.html 0000644 0002441 0001757 00000003064 11606605730 013755 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Active sequence collection (ASC)
A collection of active protein sequences, or protein fragments or subsequences, collected in the form of function-oriented databases. The sequences have known biological activity.
website/aspicdb.html 0000644 0002441 0001757 00000007652 11606605730 014623 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Alternative splicing prediction database (ASPICdb)
A database designed to provide access to reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano' et al. 2006), and to the functional annotation of predicted isoforms.
Available data
Example queries
website/astd.html 0000644 0002441 0001757 00000037534 11606605730 014153 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Alternative splicing and transcript diversity (ASTD) database
Alternative splicing and transcript diversity.
Available data
Example queries
website/atcc_dna.html 0000644 0002441 0001757 00000002503 11606605730 014740 0 ustar jison industry
Bioinformatics Data Resource Catalogue
American type culture collection database (ATCC)
ATCC cultures and bioproducts.
website/atcc.html 0000644 0002441 0001757 00000004337 11606605730 014125 0 ustar jison industry
Bioinformatics Data Resource Catalogue
American type culture collection database (ATCC)
ATCC cultures and bioproducts.
Available data
Example queries
| Data |
Format |
Query |
Example |
website/atcc_in_host.html 0000644 0002441 0001757 00000002512 11606605730 015641 0 ustar jison industry
Bioinformatics Data Resource Catalogue
American type culture collection database (ATCC)
ATCC cultures and bioproducts
website/athamap.html 0000644 0002441 0001757 00000003474 11606605730 014627 0 ustar jison industry
Bioinformatics Data Resource Catalogue
AthaMap database of Arabidopsis TFBS predictions
Genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis thaliana.
website/atsd.html 0000644 0002441 0001757 00000002415 11606605730 014141 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Aminoacyl-tRNA synthetases database (ATSD)
Aminoacyl-tRNA synthetases database.
website/autopsi.html 0000644 0002441 0001757 00000002445 11606605730 014675 0 ustar jison industry
Bioinformatics Data Resource Catalogue
AutoPSI database of predicted SCOP classifications
Predicted SCOP classifications.
website/axeldb.html 0000644 0002441 0001757 00000002512 11606605730 014443 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Axeldb database of gene expression in Xenopus laevis
Gene expression in Xenopus laevis.
website/balibase.html 0000644 0002441 0001757 00000002637 11606605730 014756 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BAliBASE benchmark alignment database
A benchmark alignment database, including enhancements for repeats, transmembrane sequences and circular permutations.
website/bcsdb.html 0000644 0002441 0001757 00000002425 11606605730 014264 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BCSDB database of bacterial carbohydrate structures
Bacterial carbohydrate structures.
website/bdgp_est.html 0000644 0002441 0001757 00000002511 11606605730 014772 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Berkeley Drosophila genome project EST database (BDGP_EST)
Berkeley Drosophila genome project EST database.
website/bdgp_ins.html 0000644 0002441 0001757 00000002756 11606605730 015003 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Berkeley Drosophila genome project database: insertion (BDGP_INS)
Berkeley Drosophila genome project database: insertion
website/bgee.html 0000644 0002441 0001757 00000035517 11606605730 014121 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Bgee database for gene expression evolution
Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomical and developmental ontologies. Then, in order to perform automated cross species comparisons, homology relationships across anatomical ontologies, and comparison criteria between developmental ontologies, are designed.
Available data
Example queries
website/bindingdb.html 0000644 0002441 0001757 00000023302 11606605730 015124 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BindingDB database of measured binding affinities
Database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
Available data
Example queries
website/biocyc.html 0000644 0002441 0001757 00000023344 11606605730 014462 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BioCyc collection of Pathway/Genome Databases
BioCyc collection of Pathway/Genome Databases. Each BioCyc database describes the genome and metabolic pathways of a single organism. This includes Escherichia coli K-12 MG1655 model-organism database (EcoCyc) and Multiorganism metabolic pathway and enzyme database (MetaCyc)
Available data
Example queries
website/biogrid.html 0000644 0002441 0001757 00000003737 11606605730 014635 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BioGRID
Physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe
website/biomodels.html 0000644 0002441 0001757 00000007461 11606605730 015171 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BioModels database of annotated published models
A that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevants, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
Available data
Example queries
website/bionumbers.html 0000644 0002441 0001757 00000003013 11606605730 015346 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BioNumbers
A database of key numbers in molecular biology, along with relevant references to the original literature, useful comments, and related numbers.
website/biosystems.html 0000644 0002441 0001757 00000003426 11606605731 015413 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BioSystems
BioSystems is a composite biological pathway and disease database and aims to: (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biological systems data.
website/bipa.html 0000644 0002441 0001757 00000007226 11606605731 014127 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BIPA database for interaction between protein and nucleic acid
Protein-nucleic acid interactions, with various features of protein-nuleic acid interfaces.
Available data
Example queries
website/bloodexpress.html 0000644 0002441 0001757 00000003242 11606605731 015717 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BloodExpress database of gene expression in mouse heamatopoesis
BloodExpress integrates 271 individual microarray experiments derived from 15 distinct studies done on most characterised mouse blood cell types. Gene expression information has been discretised to absent/present/unknown calls.
website/blotbase.html 0000644 0002441 0001757 00000007567 11606605731 015017 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BlotBase Northern blots database
Northern blots database.
Available data
Example queries
website/bndb.html 0000644 0002441 0001757 00000002514 11606605731 014114 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Biochemical network database (BNDB)
Biochemical network database for analyzing and visualizing complex biochemical networks and processes.
website/bold.html 0000644 0002441 0001757 00000003335 11606605731 014131 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Barcode of Life database (BOLD)
An online workbench that aids collection, management, analysis, and use of DNA barcodes. It consists of 3 components (MAS, IDS, and ECS) that each address the needs of various groups in the barcoding community.
Example queries
| Data |
Format |
Query |
Example |
website/brenda.html 0000644 0002441 0001757 00000012115 11606605731 014440 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BRENDA comprehensive enzyme information system
Comprehensive enzyme information.
Available data
Example queries
website/brix.html 0000644 0002441 0001757 00000002551 11606605731 014154 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BriX classification of protein fragments
BriX is a structural classification of protein fragments. The library comprises fragments ranging from 4 to 14 amino acids that are clustered against 6 different distance thresholds.
website/buchnerabase.html 0000644 0002441 0001757 00000002773 11606605731 015640 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BuchneraBase database of Buchnera species
A database designed to encapsulate and reference information obtained from the complete genome sequence of the gamma-proteobacterium Buchnera species.
website/butterflybase.html 0000644 0002441 0001757 00000003135 11606605731 016062 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ButterflyBase database of comparative Genomics of Lepidoptera
Gene database for butterflies and moths.
website/cabri.html 0000644 0002441 0001757 00000004326 11606605731 014272 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Common Access to Biotechnological Resources and Information (CABRI)
A collection of European Biological Resource Centre catalogues.
Available data
Example queries
| Data |
Format |
Query |
Example |
website/cadre.html 0000644 0002441 0001757 00000002501 11606605731 014261 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Central aspergillus data repository (CADRE)
Central aspergillus data repository (CADRE).
website/cangem.html 0000644 0002441 0001757 00000003346 11606605731 014445 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CanGEM database of clinical tumor samples and microarray data
A public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes.
website/catdb.html 0000644 0002441 0001757 00000014202 11606605731 014261 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Complete Arabidopsis transcriptome database (CATdb)
CATdb contains data on 105 Arabidopsis transcriptome projects (3262 hybridized samples) in public access out of a total of 172 projects (~6440 hybridized samples). The data are released one year after their production.
Available data
Example queries
website/cath.html 0000644 0002441 0001757 00000017514 11606605731 014134 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CATH protein structure classification database
CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis.
Available data
Example queries
website/catma.html 0000644 0002441 0001757 00000003514 11606605731 014275 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Arabidopsis transcriptome microarray database (CATMA)
The aim of the Complete Arabidopsis Transcriptome MicroArray (CATMA) project was the design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes. The GST repertoire is used by numerous groups for the production of DNA arrays for transcript profiling experiments.
website/cazy.html 0000644 0002441 0001757 00000006025 11606605731 014156 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Carbohydrate-active enzymes database (CAZy)
The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
Available data
Example queries
website/cbs.html 0000644 0002441 0001757 00000002437 11606605731 013762 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Genome atlas database (CBS)
Summary of genomic information currently available for various organisms.
website/ccap.html 0000644 0002441 0001757 00000005254 11606605731 014121 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Culture collection of algae and protozoa (CCAP)
Culture collection of algae and protozoa
Available data
Example queries
website/cc+.html 0000644 0002441 0001757 00000002431 11606605731 013645 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CC+ database of coiled-coil structures
A relational database of coiled-coil structures.
website/cdd.html 0000644 0002441 0001757 00000027204 11606605732 013745 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Conserved domain database (CDD)
A collection of multiple sequence alignments for ancient domains and full-length proteins.
Available data
Example queries
website/cellcycledb.html 0000644 0002441 0001757 00000010125 11606605731 015451 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Cell cycle database (CellCycleDB)
A collection of genes and proteins involved in human and yeast cell cycle.
Available data
Example queries
website/celllinedb.html 0000644 0002441 0001757 00000003156 11606605732 015310 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Cell line database (CellLineDB)
Information on 4.850 human and animal cell lines that are available in many Italian laboratories and in some of the most important European cell banks and cell culture collections.
website/cellmint.html 0000644 0002441 0001757 00000003045 11606605732 015017 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CellMINT database of protein localization and interactions
A database tool to integrate protein localization and interaction information.
website/centrosome:db.html 0000644 0002441 0001757 00000002614 11606605732 015767 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Centrosomal proteins database (Centrosome:db)
Centrosome:db contains a set of human genes encoding proteins that are localized in the centrosome, either as centrosome constituents or as centrosome visitors.
website/cephdb.html 0000644 0002441 0001757 00000002777 11606605732 014450 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CEPH genotype database (CEPHdb)
A database of genotypes for genetic markers that have been typed on the CEPH reference family resource for linkage mapping.
website/cgd.html 0000644 0002441 0001757 00000010041 11606605732 013737 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Candida genome database (CGD)
A resource for genomic sequence data and gene and protein information for Candida albicans.
Available data
Example queries
website/cg.html 0000644 0002441 0001757 00000010710 11606605732 013576 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Comparative genometrics (CG) database
Devoted to the characterization of complete chromosome sequences by standardized genometric methods, the Comparative Genometrics website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarly focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles.
Available data
Example queries
website/chebi.html 0000644 0002441 0001757 00000005640 11606605732 014265 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of chemical entities of biological interest (ChEBI)
Dictionary of molecular entities focused on small chemical compounds. "Molecular entity" includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.
Available data
Example queries
website/chembl.html 0000644 0002441 0001757 00000003074 11606605732 014444 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ChEMBL
A database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).
website/chemidplus.html 0000644 0002441 0001757 00000003347 11606605732 015352 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ChemIDplus
Structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases, including the TOXNET® system. ChemIDplus also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.
website/citexplore.html 0000644 0002441 0001757 00000007236 11606605732 015374 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CiteXplore literature database
CiteXplore combines literature search with text mining tools for biology.
Available data
Example queries
website/cleanex.html 0000644 0002441 0001757 00000010463 11606605732 014631 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CleanEx database of gene expression profiles
Public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.
Available data
Example queries
website/clima.html 0000644 0002441 0001757 00000010517 11606605732 014277 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database for cell line integrated molecular authentication (CLIMA)
Cell line integrated molecular authentication.
Available data
Example queries
website/clustr.html 0000644 0002441 0001757 00000003051 11606605732 014521 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CluSTr protein classification database
Automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences.
website/cmd.html 0000644 0002441 0001757 00000007311 11606605732 013753 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Collagen Mutation Database (CMD)
Database of osteogenesis imperfecta and type III collagen variants.
Available data
Example queries
website/cmr.html 0000644 0002441 0001757 00000016276 11606605732 014003 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Comprehensive microbial genome resource (CMR)
Information on all of the publicly available, complete prokaryotic genomes. Common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes.
Available data
Example queries
website/cogeme.html 0000644 0002441 0001757 00000007566 11606605732 014463 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Phytopathogenic fungi and oomycete EST database (COGEME)
Phytopathogenic fungi and oomycete EST database.
Available data
Example queries
website/colibase.html 0000644 0002441 0001757 00000003216 11606605732 014771 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ColiBase Enterobactericaiae genome database
A database for comparative genome analysis of Enterobactericaiae, e.g. Escherichia, Shigella etc..
website/columba.html 0000644 0002441 0001757 00000003103 11606605732 014625 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Columba protein structure annotation database
Annotations for protein structures from the Protein Data Bank (PDB) from several protein structure related sources, including KEGG and ENZYME. The calculated secondary structure from DSSP is included as well as the protein-fold classification databases SCOP and CATH. Further functional and taxonomic annotation is available from Swiss-Prot, the Gene Ontology (GO) and the NCBI Taxonomy.
website/compluyeast-2dpage.html 0000644 0002441 0001757 00000007633 11606605732 016724 0 ustar jison industry
Bioinformatics Data Resource Catalogue
COMPLUYEAST-2DPAGE database
A two-dimensional polyacrilamide gel electrophoresis federated database.
Available data
Example queries
website/conoserver.html 0000644 0002441 0001757 00000005664 11606605732 015406 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Cone snail toxin database (ConoServer)
Conotoxin peptide sequences and structures.
Available data
Example queries
website/consensuspathdb.html 0000644 0002441 0001757 00000017514 11606605733 016422 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ConsensusPathDB database of human functional interaction networks
Information on physical molecular interactions, biochemical pathways, and gene regulatory networks in human.
Available data
Example queries
website/corg.html 0000644 0002441 0001757 00000003107 11606605733 014142 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Comparative regulatory genomics database (CORG)
Conserved non-coding blocks from a collection of vertebrate species. Non-coding DNA segments that are conserved across multiple homologous genomic sequences are good indicators of putative regulatory elements.
website/cornea-2dpage.html 0000644 0002441 0001757 00000007551 11606605733 015626 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human cornea 2-DE database (Cornea-2DPAGE)
Two-dimensional polyacrylamide gel electrophoresis federated database.
Available data
Example queries
website/corum.html 0000644 0002441 0001757 00000006371 11606605733 014343 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CORUM comprehensive resource of mammalian protein complexes
The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.
Available data
Example queries
website/coryneregnet4.html 0000644 0002441 0001757 00000003300 11606605733 015773 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CoryneRegNet 4.0 cornyebacterial gene regulation database
Reference database for cornyebacterial transcription factors and gene regulatory networks.
website/cosmic.html 0000644 0002441 0001757 00000002532 11606605733 014466 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Catalogue of somatic mutations in cancer (COSMIC)
Somatic mutation information and related details and information relating to human cancers.
website/cpath.html 0000644 0002441 0001757 00000002670 11606605752 014314 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Pathway Commons database
A collection of publicly available pathways from multiple organisms. It provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.
website/crest.html 0000644 0002441 0001757 00000003211 11606605733 014324 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Crop ESTs database (CREST)
Sequence, classification, clustering, and annotation data of crop EST projects.
website/crisprdb.html 0000644 0002441 0001757 00000003167 11606605733 015026 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of clustered regularly interspaced short palindromic repeats (CRISPRdb)
Clustered regularly interspaced short palindromic repeats.
website/csa.html 0000644 0002441 0001757 00000002655 11606605733 013765 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Catalytic site atlas (CSA)
Catalytic sites in proteins.
website/csdbase.html 0000644 0002441 0001757 00000002574 11606605733 014623 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of cold shock domain (CSD)-containing proteins (CSDBase)
An interactive database for cold shock domain (CSD) containing proteins and the bacterial cold shock response.
website/ctd.html 0000644 0002441 0001757 00000006036 11606605733 013766 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Comparative Toxicogenomics Database (CTD)
CTD includes manually curated data describing cross-species chemical–gene/protein interactions and chemical– and gene–disease relationships to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases.
Available data
Example queries
website/cuticledb.html 0000644 0002441 0001757 00000006172 11606605733 015153 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Structural proteins of the arthropod cuticle (CuticleDB)
A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif responsible for chitin binding in Arthropod cuticle.
Available data
Example queries
website/cyclebase.html 0000644 0002441 0001757 00000002410 11606605733 015136 0 ustar jison industry
Bioinformatics Data Resource Catalogue
CycleBase cell cycle database
A standardized resource for researchers to inspect and download cell-cycle datasets.
website/cygd.html 0000644 0002441 0001757 00000006546 11606605733 014150 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Comprehensive yeast genome database (CYGD)
Information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.
Available data
Example queries
website/cymobase.html 0000644 0002441 0001757 00000002660 11606605733 015015 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database for cytoskeletal and motor proteins (CyMoBase)
Structure, function and phylogeny of cytoskeletal and motor proteins.
website/cytokine.html 0000644 0002441 0001757 00000002666 11606605733 015046 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Cytokine gene polymorphism database
Cytokine gene polymorphism in human disease.
website/dali.html 0000644 0002441 0001757 00000002775 11606605733 014133 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Dali database of 3D structure alignments
The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB). The structural neighbourhoods and alignments are automatically maintained and regularly updated using the Dali search engine.
website/dbali.html 0000644 0002441 0001757 00000002347 11606605733 014270 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DBAli structure alignment database
Database of protein structure alignments.
website/dbd.html 0000644 0002441 0001757 00000005450 11606605733 013744 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Transcription factor prediction database (DBD)
Predicted transcription factors in completely sequenced genomes.
Available data
Example queries
website/dbest.html 0000644 0002441 0001757 00000026427 11606605733 014323 0 ustar jison industry
Bioinformatics Data Resource Catalogue
dbEST database of EST sequences
dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
Available data
Example queries
website/dbprobe.html 0000644 0002441 0001757 00000006275 11606605733 014636 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NCBI Probe database of nucleic acid reagents (dbProbe)
Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.
Available data
Example queries
website/dbsnp.html 0000644 0002441 0001757 00000005450 11606605734 014322 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of single nucleotide polymorphism (dbSNP)
Single nucleotide polymorphisms.
Available data
Example queries
website/ddbj.html 0000644 0002441 0001757 00000007552 11606605734 014124 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DNA databank of Japan (DDBJ)
A nucleotide sequence database.
Available data
Example queries
website/degradome.html 0000644 0002441 0001757 00000002366 11606605734 015146 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Degradome database of mammalian proteases and diseases
Mammalian proteases and diseases.
website/diamond.html 0000644 0002441 0001757 00000014562 11606605734 014633 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Blackfan Anemia mutation database (Diamond)
Blackfan Anemia mutation database.
Available data
Example queries
website/diark.html 0000644 0002441 0001757 00000002613 11606605734 014304 0 ustar jison industry
Bioinformatics Data Resource Catalogue
diArk eukaryotic genome research database
Database for eukaryotic sequencing projects.
website/diatom.html 0000644 0002441 0001757 00000002746 11606605734 014476 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Diatom EST database
A searchable databases of diatom ESTs (expressed sequence tags) that can be used to explore diatom biology. Diatoms are photosynthetic unicellular eukaryotes that play an essential role in marine ecosystems. On a global scale, they generate around one fifth of the oxygen we breathe.
website/dictybase.html 0000644 0002441 0001757 00000006304 11606605734 015162 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Dictyostelium discoideum online informatics resource (dictyBase)
Database for the biology and genomics of the social amoeba Dictyostelium discoideum.
Available data
Example queries
website/dima.html 0000644 0002441 0001757 00000005415 11606605734 014127 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DIMA domain interaction map
Functional and physical interactions among conserved protein-domains, including experimental data and computational predictions.
Available data
Example queries
website/dip.html 0000644 0002441 0001757 00000006323 11606605734 013770 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of interacting proteins (DIP)
The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.
Available data
Example queries
website/diprodb.html 0000644 0002441 0001757 00000006730 11606605734 014641 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Dinucleotide property database (DiProDB)
The Dinucleotide Property Database is designed to collect and analyse thermodynamic, structural and other dinucleotide properties. The table presenting all the dinucleotide properties can be pruned and rearranged by different criteria. The database contains different export and analysis functions.
Available data
Example queries
website/disprot.html 0000644 0002441 0001757 00000005670 11606605734 014704 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of protein disorder (DisProt)
A curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.
Available data
Example queries
website/dnareplication.html 0000644 0002441 0001757 00000002347 11606605734 016212 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DNA replication database
A Resource for eukaryotic DNA replication.
website/dockground.html 0000644 0002441 0001757 00000002537 11606605734 015356 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Dockground database for molecular modelling of protein interactions
Benchmarks, decoys, templates and other knowledge resources for docking.
website/domino.html 0000644 0002441 0001757 00000002617 11606605734 014503 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DOMINO domain peptide interactions database
Database of annotated experiments describing interactions mediated by protein-interaction domains.
website/doop.html 0000644 0002441 0001757 00000002750 11606605734 014155 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of orthologous promoters (DoOP)
A database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species.
website/dosac-cobs-2dpage.html 0000644 0002441 0001757 00000005516 11606605734 016374 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DOSAC-COBS 2D-PAGE database
Two-dimensional polyacrylamide gel electrophoresis federated database.
Available data
Example queries
website/dpdb.html 0000644 0002441 0001757 00000002647 11606605734 014132 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Drosophila polymorphism database (DPDB)
A collection of all the existing polymorphic sequences in the Drosophila genus. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity.
website/dpvweb.html 0000644 0002441 0001757 00000011363 11606605734 014503 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DPVweb database of plant viruses
Information about viruses, viroids and satellites of plants, fungi and protozoa, with some additional data on related animal viruses.
Available data
Example queries
website/dqcs.html 0000644 0002441 0001757 00000002522 11606605734 014143 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The Database of Quantitative Cellular Signaling
A repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models.
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ID EuroPhenome
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ID ExTopoDB
ID EyeSite
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ID FANTOM_DB
ID FASTDB
ID FCP
ID FGDB
ID FINDBase
ID FireDB
ID FLAGdb++
ID FLIGHT
ID FlyBase
ID FlyMine
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ID FlyTF
ID FlyView
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ID GreenPhylDB
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ID H-InvDB
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ID HAMAP
ID HAMASTERS
ID HCAD
ID HepSeq
ID HERVd
ID HGDP-CEPH
ID HGMD
ID HGNC
ID HGT-DB
ID HGVbaseG2P
ID HIC-Up
ID HmtDB
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ID HOVERGEN
ID HomeoboxPage
ID HomoMINT
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PMID 18628892
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ID UniHI
ID UNILIB
ID Unipathway
ID UniSave
ID UniSTS
ID UNITE
ID UniTrap
ID UMD
ID UniParc
ID UniProt
ID UniProtKB/Swiss-Prot
ID UniProtKB/TrEMBL
ID UniRef
ID UTILLdb
ID UTRdb
ID UTRsite
ID VBASE2
ID VectorBase
ID VEGA
ID VIDA
ID VirusMINT
ID VSGdb
ID WorfDB
ID World-2DPAGE
ID WormBase
ID Xenbase
ID Yeast complexes
ID Yeast-GFP
ID YEASTRACT
ID YGOB
ID yMGV
ID ZFIN
website/drcatindex.html 0000644 0002441 0001757 00000171565 11607011764 015347 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DRCAT Resource Catalogue
Bioinformatics Web-based Data Resources
0, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z
- 2dpage - 2D-PAGE proteome database system for microbial research
- 3dgenomics - 3D-Genomics database of structural annotations for proteomes
- 3did - 3DID database of 3D interacting domains
- 3dmet - 3DMET
- 4dxpress - 4DXpress cross species gene expression pattern database
- 5srrna - 5S rRNA database
- a1atvar - A1ATVar A1-antitrypsin database
- aarhus_ghent-2dpage - Human keratinocyte 2D gel protein database from Aarhus and Ghent universities
- abcdb - Archaeal and bacterial ABC transporter database (ABCdb)
- abs - ABS database of binding sites from orthologous promoters
- aceview - AceView genes database
- aclame - ACLAME classification of mobile genetic elements
- affindb - Affinity database (AffinDB) for protein ligand complexes
- aftol - Assembling the Fungal Tree of Life (AFTOL) database
- agd - Ashbya genome database (AGD)
- allergome - Allergome; a platform for allergen knowledge
- amypdb - Amyloid precursor proteins database (AMYPDB)
- anpr - Arabidopsis nucleolar protein database (ANPR)
- antibodypedia - Antibodypedia database of antibodies to human proteins
- antijen - AntiJen database for peptides binding to immunity related proteins
- anu-2dpage - Australian National University 2-DE database (ANU-2DPAGE)
- aphidbase - Aphid genome database (AphidBase)
- apid - Agile protein interaction data analyzer (APID)
- eupathdb - Apicomplexan database resources (ApiDB)
- apidb_cryptodb - Cryptosporidium genome resources (CryptoDB)
- apidb_plasmodb - Plasmodium genome resources (PlasmoDB)
- apidb_toxodb - Toxoplasma genome resources (ToxoDB)
- apidb_trichdb - Trichomonas genome resources (TrichDB)
- apidb_tritrypdb - Kinetoplastid genome resources (TritryPDB)
- apidb_giardiadb - Giardia genome resources (GiardiaDB)
- appadb - Pristionchus.org P. pacificus database (AppaDB)
- arachnoserver - ArachnoServer
- arac-xyls - AraC-XylS database of a family of Helix-Turn-Helix transcription factors from bacteria
- aramemnon - ARAMEMNON database of plant membrane proteins
- archdb - ArchDB database of loop structures
- argonaute - Argonaute database of mammalian microRNAs regulatory function
- arrayexpress - ArrayExpress repository for microarray data
- asap - Systematic annotation package for community analysis of genomes (ASAP)
- asc - Active sequence collection (ASC)
- aspicdb - Alternative splicing prediction database (ASPICdb)
- astd - Alternative splicing and transcript diversity (ASTD) database
- atcc - American type culture collection database (ATCC)
- atcc_in_host - American type culture collection database (ATCC)
- atcc_dna - American type culture collection database (ATCC)
- atsd - Aminoacyl-tRNA synthetases database (ATSD)
- athamap - AthaMap database of Arabidopsis TFBS predictions
- autopsi - AutoPSI database of predicted SCOP classifications
- axeldb - Axeldb database of gene expression in Xenopus laevis
- balibase - BAliBASE benchmark alignment database
- bcsdb - BCSDB database of bacterial carbohydrate structures
- bdgp_est - Berkeley Drosophila genome project EST database (BDGP_EST)
- bdgp_ins - Berkeley Drosophila genome project database: insertion (BDGP_INS)
- bgee - Bgee database for gene expression evolution
- bindingdb - BindingDB database of measured binding affinities
- biocyc - BioCyc collection of Pathway/Genome Databases
- biogrid - BioGRID
- biomodels - BioModels database of annotated published models
- bionumbers - BioNumbers
- biosystems - BioSystems
- bipa - BIPA database for interaction between protein and nucleic acid
- bloodexpress - BloodExpress database of gene expression in mouse heamatopoesis
- blotbase - BlotBase Northern blots database
- bndb - Biochemical network database (BNDB)
- bold - Barcode of Life database (BOLD)
- brenda - BRENDA comprehensive enzyme information system
- brix - BriX classification of protein fragments
- buchnerabase - BuchneraBase database of Buchnera species
- butterflybase - ButterflyBase database of comparative Genomics of Lepidoptera
- cabri - Common Access to Biotechnological Resources and Information (CABRI)
- cadre - Central aspergillus data repository (CADRE)
- cangem - CanGEM database of clinical tumor samples and microarray data
- catdb - Complete Arabidopsis transcriptome database (CATdb)
- cath - CATH protein structure classification database
- catma - Arabidopsis transcriptome microarray database (CATMA)
- cazy - Carbohydrate-active enzymes database (CAZy)
- cbs - Genome atlas database (CBS)
- cc+ - CC+ database of coiled-coil structures
- ccap - Culture collection of algae and protozoa (CCAP)
- cellcycledb - Cell cycle database (CellCycleDB)
- celllinedb - Cell line database (CellLineDB)
- cellmint - CellMINT database of protein localization and interactions
- centrosome:db - Centrosomal proteins database (Centrosome:db)
- cephdb - CEPH genotype database (CEPHdb)
- cg - Comparative genometrics (CG) database
- cdd - Conserved domain database (CDD)
- cgd - Candida genome database (CGD)
- chebi - Database of chemical entities of biological interest (ChEBI)
- chembl - ChEMBL
- chemidplus - ChemIDplus
- citexplore - CiteXplore literature database
- cleanex - CleanEx database of gene expression profiles
- clima - Database for cell line integrated molecular authentication (CLIMA)
- clustr - CluSTr protein classification database
- cmr - Comprehensive microbial genome resource (CMR)
- cogeme - Phytopathogenic fungi and oomycete EST database (COGEME)
- colibase - ColiBase Enterobactericaiae genome database
- cmd - Collagen Mutation Database (CMD)
- columba - Columba protein structure annotation database
- compluyeast-2dpage - COMPLUYEAST-2DPAGE database
- conoserver - Cone snail toxin database (ConoServer)
- consensuspathdb - ConsensusPathDB database of human functional interaction networks
- corg - Comparative regulatory genomics database (CORG)
- corum - CORUM comprehensive resource of mammalian protein complexes
- coryneregnet4 - CoryneRegNet 4.0 cornyebacterial gene regulation database
- cosmic - Catalogue of somatic mutations in cancer (COSMIC)
- cornea-2dpage - Human cornea 2-DE database (Cornea-2DPAGE)
- crest - Crop ESTs database (CREST)
- crisprdb - Database of clustered regularly interspaced short palindromic repeats (CRISPRdb)
- csa - Catalytic site atlas (CSA)
- csdbase - Database of cold shock domain (CSD)-containing proteins (CSDBase)
- ctd - Comparative Toxicogenomics Database (CTD)
- cuticledb - Structural proteins of the arthropod cuticle (CuticleDB)
- cyclebase - CycleBase cell cycle database
- cygd - Comprehensive yeast genome database (CYGD)
- cymobase - Database for cytoskeletal and motor proteins (CyMoBase)
- cytokine - Cytokine gene polymorphism database
- dali - Dali database of 3D structure alignments
- dbali - DBAli structure alignment database
- dbd - Transcription factor prediction database (DBD)
- dbest - dbEST database of EST sequences
- dbprobe - NCBI Probe database of nucleic acid reagents (dbProbe)
- dbsnp - Database of single nucleotide polymorphism (dbSNP)
- ddbj - DNA databank of Japan (DDBJ)
- degradome - Degradome database of mammalian proteases and diseases
- diamond - Blackfan Anemia mutation database (Diamond)
- diark - diArk eukaryotic genome research database
- diatom - Diatom EST database
- dictybase - Dictyostelium discoideum online informatics resource (dictyBase)
- dima - DIMA domain interaction map
- dip - Database of interacting proteins (DIP)
- diprodb - Dinucleotide property database (DiProDB)
- disprot - Database of protein disorder (DisProt)
- dnareplication - DNA replication database
- dockground - Dockground database for molecular modelling of protein interactions
- domino - DOMINO domain peptide interactions database
- doop - Database of orthologous promoters (DoOP)
- dosac-cobs-2dpage - DOSAC-COBS 2D-PAGE database
- dpdb - Drosophila polymorphism database (DPDB)
- dpvweb - DPVweb database of plant viruses
- dqcs - The Database of Quantitative Cellular Signaling
- drc - Database of ribosomal crosslinks (DRC)
- drugbank - DrugBank drug and drug target database
- dsd - Database of dehydrogenase stereospecificities (DSD)
- dsmm - Database of simulated molecular motions (DSMM)
- dssp - DSSP secondary structure database
- dynaprot - DynaProt 2D proteome database of Lactococcus lactis
- eased - EASED database
- ecid - E Coli predicted protein interactions database (EcID)
- eco2dbase - 2D-PAGE database of Escherichia coli
- 2dbase-ecoli - 2D-PAGE database of Escherichia coli
- ecogene - EcoGene database of Escherichia coli sequence and function
- echobase - EchoBASE: an integrated post-genomic database for E. coli
- emap - Edinburgh Mouse Atlas project database (emap)
- eds - Electron density server at Uppsala university (EDS)
- ega - European genome-phenome Archive (EGA)
- eggnog - Database of evolutionary genealogy of genes: non-supervised Orthologous Groups (eggNOG)
- elm - Eukaryotic linear motif resource (ELM)
- embl - The EMBL Nucleotide Sequence Database (EMBL)
- emdb - Electron microscopy databank (EMDB)
- emglib - Enhanced microbial genomes library (EMGlib)
- ena - European nucleotide short read and trace archive (ENA)
- endonet - Endocrine networks database (EndoNet)
- ensembl - Ensembl eukaryotic genome annotation project
- ensembl-genome - Ensembl-Genome
- ensemblbacteria - Ensembl bacterial genome annotation project
- ensemblfungi - Ensembl gungial genome annotation project
- ensemblmetazoa - Ensembl invertebrate metazoan genome annotation project
- ensemblplants - Ensembl plant genome annotation project
- ensemblprotists - Ensembl protist genome annotation project
- enzyme - Enzyme nomenclature database (ENZYME)
- epd - Eukaryotic promoter database (EPD)
- eric - Enteropathogen resource integration center (ERIC)
- esldb - Eukaryotic subcellular localization database (eSLDB)
- esp-soldb - Genomic generic database applied to tomato fruit quality (ESP-SOLDB)
- esther - ESTHER database on alpha/beta hydrolases
- euhcvdb - European Hepatitis C virus database (euHCVdb)
- europhenome - EuroPhenome mouse phenotype resource
- everest - Evolutionary ensembles of recurrent segments (EVEREST)
- explorenz - ExplorEnz enzyme database
- exprot - Database for proteins with an experimentally verified function (EXProt)
- extopodb - Experimentally derived topological models of transmembrane proteins (ExTopoDB)
- eyesite - EyeSite eye protein database
- facd - Familial cancer database (FaCD)
- fantom_db - Database of functional annotation of mammalian Genome (FANTOM_DB)
- fastdb - Friendly alternative splicing and transcripts database (FASTDB)
- fcp - Functional coverage of the proteome (FCP)
- fgdb - Fusarium graminearum genome database (FGDB)
- findbase - FINDBase
- firedb - Database of functionally important residues from protein structures (FireDB)
- flagdb++ - FLAGdb++ a database for the functional analysis of the Arabidopsis genome
- flight - FLIGHT database integrating genomic and high-throughput data
- flybase - FlyBase database of genetic and molecular data of Drosophila
- flymine - FlyMine Drosophila genome database
- flysnp - SNPs database for Drosophila (FLYSNP)
- flytf - FlyTF Drosophila Site-Specific Transcription Factor Database
- flyview - FlyView database
- fpspd - Functional protein sequence pattern database (FPSPD)
- funcoup - FunCoup database
- fungalgenomesize - Fungal genome size database
- funpep - FUNPEP information system for "low complexity sequence regions"
- funshift - FunShift database
- funsimmat - FunSimMat database of semantic and functional similarity
- funybase - FUNYBASE fungal phylogenomic database
- fusiondb - FusionDB database of bacterial and archaeal gene fusion events
- g2cdb - Genes to cognition database (G2Cdb)
- gabipd - GabiPD: primary database of plant integrative biology
- gabi-kat - GABI-Kat tags mutagenised A. thaliana
- gbiffi - Global biodiversity information facility, Finland (GBIFFI)
- gdb - Human Genome Database (GDB)
- genatlas - GenAtlas human gene database
- genbank - GenBank nucleotide sequence database
- genbank-dbsts - STS database maintained at the NCBI (dbSTS)
- gene3d - Gene3D structural and functional annotation of protein families
- geneannot - Affymetrix probe-sets database (GeneAnnot)
- genecards - GeneCards database of human genes, protein and diseases
- genedb - GeneDB database from Sanger Institute Pathogen Sequencing Units
- genedb_spombe - Schizosaccharomyces pombe genome database (GeneDB_Spombe)
- geneexpressiontooth - Gene expression in tooth database
- genefarm - GeneFarm annotation of Arabidopsis thaliana gene and protein families
- geneid - GeneID database of genes from NCBI RefSeq genomes
- geneloc - GeneLoc map for human chromosomes
- genenest - GeneNest transcript clusters
- genenote - GeneNote human genes and their expression profiles
- genesapiens - GeneSapiens human transcriptome database
- genesnps - SNPs Program at the University of Washington (GeneSNPs)
- genetide - GeneTide database
- genetree - GeneTree
- genevestigator - Genevestigator
- genolevures - Genolevures 18 yeast genomes
- genolist - GenoList comparative analysis of microbial genomes
- genomereviews - GenomeReviews database of completely sequenced genomes
- genomicthreadingdatabase - Genomic threading database
- genomernai - GenomeRNAi database
- germlinep53mutations - Germline p53 Mutations database
- germonline - Gametogenesis and reproductive tissue expression
- glycatebase - GlycateBase glycation prediction
- glycomedb - Glycome database
- glycosuitedb - GlycoSuiteDB glycan database
- go - Gene ontology
- goa - Gene ontology annotation database for UniProt (GOA-UniProt)
- gold - Genomes database
- golddb - GOLDDB database of genomics of lipid-associated disorders
- gopubmed - GoPubMed ontology-based literature search
- gpcrdb - Information system for G protein-coupled receptors (GPCRs)
- gpcr_nava - GPCR natural variants database
- glycosciencesdb - Glycosciences database
- gpdb - A database of G-proteins,GPCRs,effectors and their interactions
- gramene - Gramene database for comparative grass genomics
- greenphyldb - A phylogenomic database for plant comparative genomics
- grin - Germplasm Resources Information Network (GRIN)
- gydb - Gypsy database of mobile genetic elements
- h-invdb - H-InvDB integrated database of human genes and transcripts
- haemb - Haemophilia B Mutation Database
- hamap - High-quality automated and manual annotation of microbial proteomes (HAMAP)
- hamasters - Haemophilia A FVIII mutation database (HAMASTERS)
- hcad - Human chromosome aberration database (HCAD)
- hepseq - HepSeq international repository for Hepatitis B virus strain data
- hervd - Human endogenous retrovirus database (HERVd)
- hgdp-ceph - HGDP-CEPH diversity panel database (HGDP-CEPH)
- hgmd - Human gene mutation database (HGMD)
- hgnc - Human gene nomenclature database (HGNC)
- hgt-db - Horizontal gene transfer-database (HGT-DB)
- hgvbaseg2p - Human Genome Variation database of Genotype-to-Phenotype information (HGVbaseG2P)
- hic-up - Hetero-compound information (HIC-Up)
- hmtdb - Human mitochondrial genomic database (HmtDB)
- hogenom - Database of homologous sequences from complete genomes (HOGENOM)
- hoinvgen - Homologous invertebrate genes database (HOINVGEN)
- hovergen - Homologous vertebrate genes database (HOVERGEN)
- homeoboxpage - HomeoboxPage homeobox gene page
- homomint - HomoMINT inferred human protein interaction network
- homstrad - Homologous structure alignment database (HOMSTRAD)
- hoppsigen - Homologous processed pseudogenes database (Hoppsigen)
- horde - Human olfactory receptor data explorer (HORDE)
- hotsprint - Computational Hot Spots of Protein Interfaces (HotSprint) database
- hpa - Human protein atlas (HPA) of expression and localization of proteins
- hs3d - Homo sapiens splice sites dataset (HS3D)
- hssp - Homology-derived secondary structure of proteins database (HSSP)
- htpselex - HTPSELEX database of high-throughput SELEX libraries for transcription factor binding sites
- huge - Human unidentified gene-encoded large proteins database (HUGE)
- humanpax6 - Human PAX6 allelic variant database (HumanPAX6)
- hmdb - Human Metabolome Database (HMDB)
- humanmtdb - Human mitochondrial genome database (HumanMtDB)
- husida - Human siRNA database
- hvrbase++ - HvrBase++ phylogenetic database for primate species
- hypercat - Bacillus cereus group Typing Database (HyperCAT)
- hypercldb - HyperCLDB cell line database
- iarctp53 - IARC TP53 mutation database
- idbases - IDbases immunodeficiency mutation databases
- idbases-btkbase - BTKbase database of X-linked agammaglobulinemia (XLA) mutations
- imgt - The international immunogenetics database (IMGT)
- imgt_hla - IMGT database of human MHC
- imgt_3dstructure-db - IMGT 3D structure database for immunoglobulins (IG), T cell receptors (TR), MHC and RPI
- imgt_gene-db - IMGT gene database for immunoglobulins (IG) and T cell recetors (TR)
- imgt_ligm - IMGT nucleotide sequence database for immunoglobulins (IG) and T cell recetors (TR)
- imgt_primer-db - IMGT primer database for immunoglobulins (IG) and T cell recetors (TR)
- infevers - Familial mediterranean fever (FMF) mutations database (INFEVERS)
- inparanoid - Inparanoid orthologs database
- intact - IntAct protein interaction database and analysis system
- integr8 - Integr8 genome and proteome database
- integrall - INTEGRALL integron integrases and gene cassettes
- intenz - Integrated relational enzyme database (IntEnz)
- interpro - InterPro integrated database of protein families, domains, regions, repeats and functional sites
- icd - International Classification of Diseases
- icds - Interrupted coding sequences (ICDS)
- ipd - Immuno polymorphism database (IPD)
- ipd-estdab - Immuno polymorphism EST database (IPD-ESTDAB)
- ipd-hpa - Immuno polymorphism human platelet antigens database (IPD-HPA)
- ipd-kir - Immuno polymorphism killer-cell Immunoglobulin-like receptor database (IPD-KIR)
- ipd-mhc - Immuno polymorphism major histocompatibility complex database (IPD-MHC)
- ipi - International protein index (IPI)
- irefindex - iRefIndex index of consolidated protein interactions
- iresdb - Internal ribosome entry site database (IRESdb)
- iresite - Database of experimentally verified IRES structures (IRESite)
- isfinder - Insertion sequence elements database (ISfinder)
- isola - Italian Solanaceae genome resource (ISOLA)
- its2 - Internal transcribed spacer 2 sequences (ITS2)
- ittaca - Integrated tumor transcriptome array and clinical data analysis (ITTACA)
- iupac - IUPAC nomenclature database
- iuphar-db - IUPHAR database
- ixdb - Integrated X chromosome database (IXDB)
- jail - JAIL structure-based interface library for macromolecules
- jaspar - JASPAR eukaryotic transcription factor binding profiles
- jcm - Japan collection of microorganisms
- jenalib - Jena library of biological macromolecules (JenaLib)
- jpgv - Jena prokaryotic genome viewer (JPGV)
- jws - JWS Online
- karyotypedb - Karyotype features from different animals and plants
- kegg - Kyoto encyclopedia of genes and genomes (KEGG)
- kdd - Kidney development database
- kinmutbase - KinMutBase registry of disease-causing mutations in protein kinase domains database
- kinomer - Kinomer database
- knottin - KNOTTIN database
- l1base - LINE-1 human and rodent
- leger - LEGER genome database for Listeria research
- legiolist - Legionella pneumophila genome database
- leproma - Mycobacterium leprae genome database
- lgicdb - Ligand-gated ion channel database (LGICdb)
- ligasite - Ligand attachment site database (LigAsite)
- lipidbank - LipidBank
- lmsd - LIPID MAPS Structure Database (LMSD)
- lipaseengineering - Lipase engineering database
- lumbribase - Lumbricus rubellus genome project database
- maizegdb - Maize genetics and genomics database (MaizeGDB)
- mamep - Molecular anatomy of mouse embryo project (MAMEP)
- mampol - Mammalia polymorphism database (MamPol)
- mapu - Max-Planck unified proteome database (MAPU)
- matdb - Arabadopsis genome database (MAtDB)
- matrixdb - MatrixDB
- macie - Mechanism, annotation and classification in enzymes (MACiE) database
- medobis - Mediterranean ocean biogeographic information system (MedOBIS)
- megx - MeGX marine microbial ecological genomics database
- mmmp - Melanoma Molecular Map Project (MMMP) i
- mepd - Medaka expression pattern database (MEPD)
- merops - MEROPS peptidase database
- metacrop - MetaCrop database of metabolic pathways in crop plants
- metagrowth - MetaGrowth database of culture conditions of obligate parasitic bacteria
- metal-macie - Metal-MACiE database of metals involved in biological catalysis
- methdb - MethDB DNA methylation database
- mfungd - MIPS mouse functional genome database (MfunGD)
- mgi - Mouse genome database (MGD) from Mouse Genome Informatics (MGI)
- micado - Microbial advanced database organisation (Micado)
- modeldb - ModelDB
- mmdb - Molecular Modeling DataBase (MMDB)
- mtrdb - Microorganisms tandem repeats database
- mim - Online Mendelian inheritance in Man (OMIM)
- mint - Molecular interaction Database (MINT)
- mipsplantsdb - MIPS plants database
- mirbase - miRBase database
- miriam - MIRIAM resources
- mirortho - miROrtho animal microRNA database
- monosaccharidedb - Monosaccharide database
- mmruv - MMR Gene Unclassified Variants Database
- mitodrome - OXPHOS genes in Drosophila
- mitop2 - Mitochondrial proteome database
- mitores - MitoRes resource for mitochondria-related genes, transcripts and proteins
- mlvabank - Bacterial MLVA-genotyping service (MLVAbank)
- mmsinc - MMsINC chemoinformatics database
- mncdb - MNCDB Neurospora crassa genome database
- modbase - ModBase database of comparative protein structure models
- modomics - Database of RNA modification pathways
- moka - MoKCa database of mutations of kinases in cancer
- molligen - MolliGen Mollicutes database
- mosaic - MOSAIC bacterial genome comparison database
- mosdb - MOsDB rice genome database
- mousesage - MouseSAGE serial analysis of gene expression database
- mousebook - MouseBook data from MRC Harwell
- mpact - MPact: Representation of Interaction Data at MIP
- mugen - MUGEN mouse database
- mumdb - MIPS Ustilago maydis Database (MUMDB)
- myhits - MyHits protein domains database
- naproc-13 - NAPROC-13 natural products 13C NMR database
- narcisse - Narcisse mirror view of conserved synteny
- nbrc - NITE biological resource center
- ncl - NCL Mutation Database
- ncrnas - ncRNAs database
- nembase - NEMBASE database for analysis of nematode ESTs
- nesbase - NESbase database of leucine-rich nuclear export signals
- neuromorpho - NeuroMorpho
- neurondb - NeuronDB
- nextbio - NextBio gene-centric data for human, mouse, rat, fly, worm and yeast
- nextdb - Nematode expression pattern dataBase (NextDB)
- nextprot - neXtProt; the human protein knowledge platform
- niaest - NIA mouse cDNA project
- nmpdr - National microbial pathogen
- nmrshift - NMRShift database of organic structure NMR spectra
- nopdb - Nucleolar proteome database (NOPDB)
- norine - NORINE database of nonribosomal peptides
- npc-db - Niemann-Pick Type C mutations
- npd - Nuclear protein database (NPD)
- nrestdb - Natural rubber EST database (NRESTdb)
- nrsub - Non-Redundant B.subtilis database (NRSub)
- nurebase - Nuclear receptor database (NUREBASE)
- oglycbase - O-GlycBase database
- ogp - Oxford glycoProteomics 2-DE database (OGP)
- oma - Identification of orthologs from complete genome data (OMA database)
- optic - Orthologous and paralogous transcripts in clades (OPTIC) database
- orenza - Database of orphan enzyme activities (ORENZA)
- orphanet - Orphanet portal for rare diseases and orphan drugs
- orthodb - Orthologous groups database (OrthoDB)
- orygenesdb - Database for rice reverse genetics (OryGenesDB)
- oryza - Oryza tag line
- osteogenesis - Osteogenesis imperfecta and type III collagen mutations
- p53famtag - p53FamTaG direct target genes
- pairsdb - PairsDB BLAST and PSI-BLAST alignments
- pandit - Protein and associated nucleotide domains with inferred trees (PANDIT)
- pandora - PANDORA visualization and annotation for protein sets
- panther - Protein analysis through evolutionary relationships (PANTHER)
- parameciumdb - Database for the model organism Paramecium tetraurelia (ParameciumDB)
- pathema - Pathema: a clade-specific bioinformatics resource
- pathoplant - PathoPlant database of plant-pathogen interactions and Arabidopsis expression
- cpath - Pathway Commons database
- pathway_interaction_db - NCI-Nature pathway interaction database
- pdb - The RCSB Protein Data Bank
- pdbe - PDBe protein structure database in Europe
- pdbfinder - PDBFINDER reformatted PDB files
- pdbfun - PDBfun annotated protein structures
- pdb-redo - PDB-redo database of re-refined PDB entries
- pdbreport - Structure validation reports for PDB entries (PDBREPORT)
- pdbselect - PDBselect database of representative PDB chains
- pdbsum - PDBsum overview of macromolecular structures
- pdbtm - Transmembrane proteins from PDB (PDBTM)
- ped - Pancreatic expression database (PED)
- pedant - PEDANT3 protein extraction, description and analysis tool
- pepseeker - PepSeeker database of proteome peptide identifications for investigating fragmentation patterns
- peptaibol - Peptaibol database of natural fungal peptides
- peptideatlas - PeptideAtlas peptide database
- peptidedb - PeptideDB database of bioactive signaling peptides
- peroxibase - PeroxiBase peroxidase family database
- peroxisomedb - Peroxisome database (PeroxisomeDB)
- pespotdb - Pepspot database (PespotDB) of peptide chip data
- pfam - Pfam protein domain database
- pgn - Plant Genome Network (PGN)
- pharmgkb - The pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)
- phenomicdb - PhenomicDB cross-species genotype/phenotype database
- phci-2dpage - Parasite host cell interaction 2D-PAGE database (PHCI-2DPAGE)
- phi-base - PHI-base pathogen host interactions database
- phosphat - Arabidopsis experimental phosphorylation sites database (PhosPhAt)
- phosphoelm - PhosphoELM database of S/T/Y phosphorylation sites
- phospho3d - PHOSPHO3D structures of phosphorylation sites
- phosphopep - PhosphoPep database of MS-derived phosphorylation data from 4 organisms
- phosphosite - Phosphorylation site database
- phossite - Phosphorylation site database for Archaea and Bacteria
- phylomedb - PhylomeDB database of phylogenetic trees for all proteins
- phylopat - PhyloPat database of phylogenetic patterns
- phytoprot - PhytoProt protein clusters database
- pips - Human protein-protein interaction prediction (PIPs)
- pir - Protein sequence database of the Protein Information Resource (PIR)
- pirsf - PIRSF whole-protein classification database
- plantdnac-values - Plant DNA C-values database (PlantDNAC-values)
- plantsnorna - Plant snoRNA database
- plantcare - Plant cis acting element
- plantmarkers - PlantMarkers database of predicted molecular markers from plants
- plant-pis - PLANT-Pis database for protease inhibitors and their genes in higher plants
- plantprom - PlantProm database of experimental plant promoter and transcription start site
- plasmodraft - Predictions of Plasmodium falciparum gene function
- plmitrna - PLMItRNA database of tRNAs in plant mitochondria
- plprot - Plastid proteins database (Plprot)
- pmap-cutdb - PMAP-CutDB proteolytic event database
- pmdb - Protein model database (PMDB)
- polymorphix - Polymorphix intraspecific sequence polymorphism database
- pomamo - PoMaMo potato maps database
- ppd - PPD protein pKa values database
- ppnema - rRNA genes from plant-parasitic nematodes (PPNEMA)
- pptasedb - Prokaryotic protein phosphatase database (PptaseDB)
- predict - preDiCT database of drug effects on the heart
- pride - PRIDE proteomics identifications database
- prints - PRINTS protein motif fingerprint database
- prism - Prism protein interaction by structural matching
- probebase - probeBase database of rRNA-targeted oligonucleotide probes
- procmd - ProCMD 3D protein C mutations database
- procognate - PROCOGNATE ligand domain mapping for enzymes
- prodom - ProDom protein domain database
- prodoric - PRODORIC prokaryotic database of gene regulation
- promec - PromEC verified E. coli promoters
- promex - ProMEX protein mass spectral library
- prophecy - PROPHECY profiling of phenotypic characteristics in yeast
- prorule - ProRule collection of rules based on PROSITE predictors
- prosas - Protein Structure and Alternative Splicing database (ProSAS)
- prosat2 - PROSAT2 protein structure annotation tool
- prosite - A Database of protein domains, families and functional sites
- protclustdb - Entrez Protein Clusters
- proteinmodelportal - Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase
- protonet - ProtoNet automatic hierarchical classification of proteins
- protepedia - Protepedia collaborative 3D protein encyclopedia
- proteus - Protein terminus short linear sequences
- pseudobase - PseudoBase RNA pseudoknots database
- pseudocap - PseudoCAP pseudomonas genome database
- pstiing - Protein, signalling, transcriptional interactions and inflammation networks gateway (pSTIING)
- ptch - PTCH mutation database
- pubchem - PubChem
- pubmeth - PubMeth reviewed methylation database in cancer
- pmma-2dpage - Purkyne Military Medical Academy 2D-PAGE database
- rat-heart-2dpage - 2-DE database of rat heart, at German Heart Institute Berlin, Germany
- ratmap - RATMAP rat genome database
- rdg - Rat genome database (RDG)
- rb1genemutation - RB1 gene mutation database (RB1GeneMutation)
- reactome - Reactome knowledgebase of biological pathways
- rebase - REBASE restriction enzymes and methylases database
- redidb - RNA editing database (REDIdb)
- refseq - NCBI reference sequences
- repairtoire - REPAIRtoire DNA repair pathways
- reproduction-2dpage - REPRODUCTION-2DPAGE database
- resid - RESID database of protein modifications
- retroryza - RetrOryza database of rice LTR retrotransposons
- rfam - RNA families database of alignments and CMs
- rgd - Rat genome database
- rhea - Rhea
- rouge - Rodent unidentified gene-encoded large proteins database (Rouge)
- rissc - Ribosomal internal spacer sequence collection (RISSC)
- rna-frabase - RNA FRABASE database
- rnavirusdb - RNA virus genome database (RNAVirusDB)
- rnrdb - Ribonucleotide reductase database (RNRdb)
- rsitedb - RNA binding site database (RsiteDB)
- rtkdb - Receptor tyrosine kinase database (RTKdb)
- rtprimerdb - PCR primers and probes database (RTPrimerDB)
- s_martdb - The S/MAR transaction database (S/MARtDB)
- s4 - S4 structure-based sequence alignments of SCOP superfamilies
- sabio-rk - Database for biochemical reactions and their kinetics.
- saffron_genes - Saffron genes database
- scop - Structural classification of proteins (SCOP) database
- scoppi - Structural Classification of Protein-Protein Interfaces (SCOPPI)
- scowl - Structural characterization of water, ligands and proteins (SCOWL)
- seattlesnps - SeattleSNPs variation discovery resource
- sebida - Sebida sex-biased genes
- seed - The SEED genome comparison environment
- selectome - Selectome database of positive selection
- sgd - Saccharomyces genome database (SGD)
- siena-2dpage - 2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy
- signalinggateway - UCSD-Nature Signaling Gateway Molecule Pages
- silva-lsu - SILVA ribosomal RNA sequence data (large subunit)
- silva-ssu - SILVA ribosomal RNA sequence data (small subunit)
- simap - Similarity matrix of proteins (SIMAP)
- sirnadb - siRNAdb database
- sisyphus - SISYPHUS database of protein structure alignments
- sitesbase - SitesBase database
- smpdb - Small Molecule Pathway Database (SMPDB)
- smart - Simple modular architecture research tool (SMART)
- smr - A database of annotated 3D protein structure models
- snap - SNAP database of human gene variations
- snappi - SNAPPI database of structures, interfaces and alignments for protein-protein interactions
- sno_scarnabase - Small nucleolar RNA and small cajal body-specific RNA database (sno/scaRNAbase)
- snornabase - snoRNABase database of human H/ACA and C/D box snoRNAs
- snpeffect - SNPeffect database of molecular phenotyping of human SNPs and disease mutations
- snpnexus - SNPnexus database for SNP selection
- snpstr - SNPSTR databasee
- source - The Stanford online universal resource for Clones and ESTs (SOURCE)
- soybase - SoyBase soybean genome database
- spliceaid - SpliceAid database of strictly experimentally assessed target RNA sequences in humans
- splicenest - SpliceNest database
- spodobase - Spodoptera frugiperda database (SpodoBase)
- stcdb - Signal transduction classification database (STCDB)
- stitch - STITCH chemical-protein interactions
- straininfo.net - StrainInfo.net bioportal
- strepto-db - Strepto-DB comparative genomics of group A and group B streptococci
- string - STRING protein-protein interaction database
- structurallyconservedinterfaces - Structurally conserved interfaces
- sulfolobus - Sulfolobus genome database
- superdrug - SuperDrug drug database
- supfam - Superfamily database of structural and functional annotation
- superhapten - SuperHapten immunogenic compound database
- supernatural - SuperNatural natural compound database
- superscent - Superscent database of scents
- supersite - SuperSite dictionary of metabolite and drug binding sites in proteins
- supertarget-matador - SuperTarget and Matador database
- supertoxic - Supertoxic toxic compounds database
- surface - SURFACE database of protein surface patches
- swiss-2dpage - Two-dimensional polyacrylamide gel electrophoresis database (SWISS-2DPAGE)
- swissregulon - SwissRegulon database of regulatory site annotations
- systers - SYSTERS protein family database
- systomonas - Systomonas database for systems biology of Pseudomonads
- sysznfc2h2 - C2H2 zinc finger gene database (SysZNFC2H2)
- t1dbase - Type 1 diabetes database (T1Dbase)
- taed - The adaptive evolution database (TAED)
- tair - The Arabidopsis information resource (TAIR)
- tarbase - miRNA target database (TarBase)
- tassdb - Tandem splice site database
- taxon - NCBI's taxonomic identifier
- tbmap - Mapping names in TreeBASE
- tcacycle - TCA cycle gene mutation database
- tcdb - Transport classification database
- tdr - TDR targets database
- 1000genomes - The 1000 Genomes project
- ttd - Therapeutic Target Database (TTD)
- tigr - The bacterial database(s) of The Institute of Genome Research
- tigrfams - A protein family database
- tmadb - Tissue microarray database
- tomatestdb - An EST database from multiple Tomato species
- topdb - Topology of transmembrane proteins
- topdom - Transmembrane domains and motifs
- t3db - Toxin and Toxin Target Database (T3DB)
- transdab - Database of transglutaminase substrate proteins
- transpath - TRANSPATH database
- transpogene - Transposed elements in proteins for 7 organisms
- trbase - Tandem repeats database
- treefam - Phylogenetic trees of animal genes
- trnasequences - tRNA sequences database
- tropgene-db - TropGENE database
- trsdb - TrSDB transcription factors
- tuberculist - Mycobacterium tuberculosis strain H37Rv genome database
- u12db - U12-type intron database
- ucd-2dpage - University College Dublin 2-DE Proteome Database
- ucsc - UCSC genome browser
- umd-dmd - UMD-DMD France genotype-phenotype dystrophinopathy patients
- unigene - UniGene gene-oriented nucleotide sequence clusters
- unihi - Unified human interactome database
- unilib - Unified library database
- unipathway - Unipathway
- unisave - Uniprot version archive
- unists - NCBI database of sequence tagged sites
- unite - UNITE rDNA sequences from ectomycorrhizal asco- and basidiomycetes
- unitrap - UniTrap gene trap clones
- umd - Universal mutation database
- uniparc - UniProt Archive
- uniprot - Universal protein resource
- uniprotkb_swiss-prot - Universal protein resource knowledge base / Swiss-Prot
- uniprotkb_trembl - Universal protein resource knowledge base / Swiss-Prot
- uniref - Non-redundant reference (UniRef) databases
- utilldb - URGV TILLING platform databases
- utrdb - Regulatory motifs in eukaryotic UTRs
- utrsite - Regulatory motifs in eukaryotic UTRs
- vbase2 - Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse
- vectorbase - Invertebrate vectors of human pathogens
- vega - Vertebrate Genome Annotation (VEGA) database
- vida - Virus Database at University College London
- virusmint - Viral protein interaction
- vsgdb - A database of trypanosomal variant surface glycoproteins
- worfdb - The C.elegans ORFeome cloning project
- world-2dpage - The world-2DPAGE database
- wormbase - Caenorhabditis elegans genome database
- world-2dpage_cgl14067-2dpage - World-wide gel-based proteomics database (CGL14067-2DPAGE)
- world-2dpage_nibr_2d-page - World-wide gel-based proteomics database (NIBR 2D-PAGE)
- world-2dpage_0003 - World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome
- world-2dpage_0004 - World-wide gel-based proteomics database (0004) for mature rat olfactory bulb
- world-2dpage_0005 - World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose
- world-2dpage_0006 - World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee
- xenbase - Xenopus laevis and tropicalis biology and genomics resource
- yeast_complexes - Yeast complexes database
- yeast-gfp - Yeast GFP fusion localization database
- yeastract - Transcriptional regulators database
- ygob - Yeast gene order browser
- ymgv - Yeast microarray global viewer
- zfin - Zebrafish information network genome database
website/drc.html 0000644 0002441 0001757 00000002562 11606605734 013765 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of ribosomal crosslinks (DRC)
Biochemical data about structure of the ribosome from ribosomal cross-linking.
website/drugbank.html 0000644 0002441 0001757 00000005440 11606605734 015010 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DrugBank drug and drug target database
Detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
Available data
Example queries
website/dsd.html 0000644 0002441 0001757 00000002621 11606605735 013764 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of dehydrogenase stereospecificities (DSD)
Database on dehydrogenases, a class of enzymes that catalyze reversible oxidation-reduction reactions and are largely dependent on nicotinamide adenine dinucleotide coenzymes: NAD(H) or NADP(H).
website/dsmm.html 0000644 0002441 0001757 00000002646 11606605735 014161 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of simulated molecular motions (DSMM)
Movies showing biomolecular motions that have been generated by computer simulation. Molecules simulated include proteins, DNA, RNA, sugars and lipids. Simulation techniques include Molecular Dynamics, Brownian Dynamics and automated docking procedures.
website/dssp.html 0000644 0002441 0001757 00000005610 11606605735 014164 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DSSP secondary structure database
Secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).
Available data
Example queries
website/dynaprot.html 0000644 0002441 0001757 00000002545 11606605735 015057 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DynaProt 2D proteome database of Lactococcus lactis
2D reference maps and summarized protein information for Lactococcus lactis.
website/eased.html 0000644 0002441 0001757 00000002346 11606605735 014277 0 ustar jison industry
Bioinformatics Data Resource Catalogue
EASED database
Extended Alternatively Spliced EST Database
website/echobase.html 0000644 0002441 0001757 00000006372 11606605735 014772 0 ustar jison industry
Bioinformatics Data Resource Catalogue
EchoBASE: an integrated post-genomic database for E. coli
A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.
Available data
Example queries
website/ecid.html 0000644 0002441 0001757 00000016360 11606605735 014123 0 ustar jison industry
Bioinformatics Data Resource Catalogue
E Coli predicted protein interactions database (EcID)
Results of running an "in silico 2 hybrid system" for all the possible pairs among E. coli proteins.
Available data
Example queries
website/eco2dbase.html 0000644 0002441 0001757 00000003035 11606605735 015041 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ECO2DBASE
2D-PAGE database of Escherichia coli
2D-PAGE database of Escherichia coli
Example queries
| Data |
Format |
Query |
Example |
website/ecogene.html 0000644 0002441 0001757 00000007235 11606605735 014625 0 ustar jison industry
Bioinformatics Data Resource Catalogue
EcoGene database of Escherichia coli sequence and function
Information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.
Available data
Example queries
website/eds.html 0000644 0002441 0001757 00000005752 11606605735 013775 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Electron density server at Uppsala university (EDS)
A service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. In addition to electron density maps and tools to view these maps, statistics and plots are provided for assessing the goodness-of-fit between the deposited models (structures) and the experimental data represented by the electron density calculated using the models and their associated structure factor amplitudes.
Available data
Example queries
website/ega.html 0000644 0002441 0001757 00000005622 11606605735 013752 0 ustar jison industry
Bioinformatics Data Resource Catalogue
European genome-phenome Archive (EGA)
A repository for all types of genotype experiments, including case control, population, and family studies, including SNP and CNV genotypes from array based methods and genotyping done with re-sequencing methods.
Available data
Example queries
website/eggnog.html 0000644 0002441 0001757 00000003364 11606605735 014465 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of evolutionary genealogy of genes: non-supervised Orthologous Groups (eggNOG)
Orthologous groups of genes. The orthologous groups are annotated with functional descriptions, which are derived by identifying a common denominator for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains.
website/elm.html 0000644 0002441 0001757 00000015441 11606605735 013773 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Eukaryotic linear motif resource (ELM)
A resource for predicting functional sites in eukaryotic proteins. Putative functional sites are identified by patterns (regular expressions). To improve the predictive power, context-based rules and logical filters are applied to reduce the amount of false positives.
Available data
Example queries
website/emap.html 0000644 0002441 0001757 00000006035 11606605735 014137 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Edinburgh Mouse Atlas project database (emap)
The emap Atlas is a digital Atlas of mouse embryonic development. It is based on the definitive books of mouse embryonic development by Theiler (1989) and Kaufman (1992) yet extends these studies by creating a series of interactive three-dimensional computer models of mouse embryos at successive stages of development with defined anatomical domains linked to a stage-by-stage ontology of anatomical names.
Available data
Example queries
website/embl.html 0000644 0002441 0001757 00000010054 11606605735 014130 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The EMBL Nucleotide Sequence Database (EMBL)
Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications.
Available data
Example queries
website/emdb.html 0000644 0002441 0001757 00000002640 11606605735 014122 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Electron microscopy databank (EMDB)
Deposition and retrieval network for cryoEM map, model and associated metadata, as well as a portal for software tools for standardized map format conversion, map, segmentation and model assessment, visualization, and data integration.
website/emglib.html 0000644 0002441 0001757 00000003625 11606605735 014456 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Enhanced microbial genomes library (EMGlib)
A database devoted to the completely sequenced bacterial genomes and the yeast genome. Starting from the sequences available in the "genome" division of GenBank, EMGlib improves and corrects the annotations.
website/ena.html 0000644 0002441 0001757 00000002375 11606605735 013763 0 ustar jison industry
Bioinformatics Data Resource Catalogue
European nucleotide short read and trace archive (ENA)
European nucleotide short read and trace archive (ENA).
website/endonet.html 0000644 0002441 0001757 00000003165 11606605735 014652 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Endocrine networks database (EndoNet)
Information about endocrine networks. Using information about hormones' donor and acceptor cells a network is built that represents hormonal signaling pathways as a bipartite graph comprising hormones and tissues as node classes. The involved components, the intercellular information flow and the inhibition or activation effects are displayed
website/ensemblbacteria.html 0000644 0002441 0001757 00000005635 11606605736 016343 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ensembl bacterial genome annotation project
Genome databases for bacterial species.
Available data
Example queries
website/ensemblfungi.html 0000644 0002441 0001757 00000005577 11606605736 015706 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ensembl gungial genome annotation project
Genome databases for fungal species.
Available data
Example queries
website/ensembl-genome.html 0000644 0002441 0001757 00000002502 11606605735 016105 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ensembl-Genome
A system for the annotation, analysis and display of vertebrate genomes and for bacteria, protists, fungi, plants and invertebrate metazoa.
website/ensembl.html 0000644 0002441 0001757 00000010273 11606605735 014641 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ensembl eukaryotic genome annotation project
Genome databases for vertebrates and other eukaryotic species.
Available data
Example queries
website/ensemblmetazoa.html 0000644 0002441 0001757 00000005647 11606605736 016234 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ensembl invertebrate metazoan genome annotation project
Genome databases for invertebrate metazoan species.
Available data
Example queries
website/ensemblplants.html 0000644 0002441 0001757 00000005610 11606605736 016063 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ensembl plant genome annotation project
Genome databases for plant species.
Available data
Example queries
website/ensemblprotists.html 0000644 0002441 0001757 00000005621 11606605736 016453 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ensembl protist genome annotation project
Genome databases for protist species.
Available data
Example queries
website/enzyme.html 0000644 0002441 0001757 00000010156 11606605736 014524 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Enzyme nomenclature database (ENZYME)
A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
Available data
Example queries
website/epd.html 0000644 0002441 0001757 00000012043 11606605736 013762 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Eukaryotic promoter database (EPD)
An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.
Available data
Example queries
website/eric.html 0000644 0002441 0001757 00000003240 11606605736 014133 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Enteropathogen resource integration center (ERIC)
Annotated enterobacterial genome and associated information.
website/esldb.html 0000644 0002441 0001757 00000003176 11606605736 014312 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Eukaryotic subcellular localization database (eSLDB)
A database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.
website/esp-soldb.html 0000644 0002441 0001757 00000002732 11606605736 015106 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Genomic generic database applied to tomato fruit quality (ESP-SOLDB)
Genomic generic database applied to tomato fruit quality (ESP-SOLDB).
website/esther.html 0000644 0002441 0001757 00000002643 11606605736 014511 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ESTHER database on alpha/beta hydrolases
Database for the analysis of protein and nucleic acid sequences belonging to the superfamily of alpha/beta hydrolases homologous to cholinesterases.
website/euhcvdb.html 0000644 0002441 0001757 00000006007 11606605736 014635 0 ustar jison industry
Bioinformatics Data Resource Catalogue
European Hepatitis C virus database (euHCVdb)
European Hepatitis C virus database.
Available data
Example queries
website/eupathdb.html 0000644 0002441 0001757 00000006545 11606605727 015020 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Apicomplexan database resources (ApiDB)
A portal for accessing genomic-scale datasets associated with the eukaryotic pathogens (Cryptosporidium, Giardia, Leishmania, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma).
Available data
Example queries
website/europhenome.html 0000644 0002441 0001757 00000002467 11606605736 015551 0 ustar jison industry
Bioinformatics Data Resource Catalogue
EuroPhenome mouse phenotype resource
Software system for capturing, storing and analysing raw phenotyping data from SOPs contained in EMPReSS.
website/everest.html 0000644 0002441 0001757 00000002441 11606605736 014670 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Evolutionary ensembles of recurrent segments (EVEREST)
An automatic identification and classification of protein domains.
website/explorenz.html 0000644 0002441 0001757 00000002753 11606605736 015247 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ExplorEnz enzyme database
The Enzyme Database with data from the IUBMB Enzyme Nomenclature List. Formatting of chemical names according to IUPAC standards is preserved.
website/exprot.html 0000644 0002441 0001757 00000003457 11606605736 014544 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database for proteins with an experimentally verified function (EXProt)
A non-redundant database of protein sequences for which the function has been experimentally verified, from Pseudomonas Community Annotation Project, from E. coli genome and proteome database and from division Prokaryotes of the EMBL Nucleotide Sequence Database.
website/extopodb.html 0000644 0002441 0001757 00000002534 11606605736 015042 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Experimentally derived topological models of transmembrane proteins (ExTopoDB)
Experimentally derived topological models of transmembrane proteins.
website/eyesite.html 0000644 0002441 0001757 00000003347 11606605736 014670 0 ustar jison industry
Bioinformatics Data Resource Catalogue
EyeSite eye protein database
An information and modelling resource for families of proteins that function in the eye. Homologues are collected from all species and clustered according to tissue type, function and sequence similarity.
website/facd.html 0000644 0002441 0001757 00000002640 11606605736 014111 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Familial cancer database (FaCD)
Database to assist clinicians and genetic counselors in making a genetic differential diagnosis in cancer patients, as well as in becoming aware of the tumor spectrum associated with hereditary disorders that have already been diagnosed in their patients.
website/fantom_db.html 0000644 0002441 0001757 00000003056 11606605736 015147 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of functional annotation of mammalian Genome (FANTOM_DB)
Functional annotation of mammalian genome.
Example queries
| Data |
Format |
Query |
Example |
website/fastdb.html 0000644 0002441 0001757 00000002365 11606605736 014463 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Friendly alternative splicing and transcripts database (FASTDB)
Alternative splicing and transcripts database.
website/fcp.html 0000644 0002441 0001757 00000002314 11606605737 013763 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Functional coverage of the proteome (FCP)
Functional coverage of the proteome.
website/fgdb.html 0000644 0002441 0001757 00000003307 11606605737 014120 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Fusarium graminearum genome database (FGDB)
Information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Fusarium graminearum (Anamorph of Gibberella zeae).
website/findbase.html 0000644 0002441 0001757 00000002443 11606605737 014771 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FINDBase
Information about the frequency of different mutations leading to inherited disorders in various populations around the globe.
website/firedb.html 0000644 0002441 0001757 00000003035 11606605737 014447 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of functionally important residues from protein structures (FireDB)
A database of Protein Data Bank structures, ligands and annotated functional site residues.
website/flagdb++.html 0000644 0002441 0001757 00000003026 11606605737 014561 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FLAGdb++ a database for the functional analysis of the Arabidopsis genome
Integrative database around plant genomes.
website/flight.html 0000644 0002441 0001757 00000003666 11606605737 014503 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FLIGHT database integrating genomic and high-throughput data
Database for the integration of data from high-throughput experiments carried out in Drosophila cell culture. It includes phenotypic information from published cell-based RNAi screens, gene expression data from Drosophila cell lines, protein interaction data, together with novel tools to cross-correlate these diverse datasets, such as the phenotype clustering tool Shuffle.
website/flybase.html 0000644 0002441 0001757 00000014147 11606605737 014647 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FlyBase database of genetic and molecular data of Drosophila
A Database of Drosophila genes and genomes.
Available data
Example queries
website/flymine.html 0000644 0002441 0001757 00000002616 11606605737 014663 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FlyMine Drosophila genome database
An integrated database for Drosophila and Anopheles genomics.
website/flysnp.html 0000644 0002441 0001757 00000002750 11606605737 014532 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SNPs database for Drosophila (FLYSNP)
Database of a high-density genome-wide map of single nucleotide polymorphisms (SNPs) and high-throughput assays for SNP genotyping.
website/flytf.html 0000644 0002441 0001757 00000002642 11606605737 014343 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FlyTF Drosophila Site-Specific Transcription Factor Database
Information on the manual curation of FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database
website/flyview.html 0000644 0002441 0001757 00000003375 11606605737 014710 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FlyView database
An image database on Drosophila development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes).The concept of FlyView includes compatibility to FlyBase, the main Drosophila database.
website/fpspd.html 0000644 0002441 0001757 00000002620 11606605737 014327 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Functional protein sequence pattern database (FPSPD)
Accumulates functional protein sequence patterns derived from the structurally-aligned homologous families in the HOMSTRAD database.
website/funcoup.html 0000644 0002441 0001757 00000004065 11606605737 014677 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FunCoup database
FunCoup is a statistical framework of data integration for finding functional coupling (FC) between proteins. It transfers information from model organisms (M. musculus, D. melanogaster, C. elegans, S. cerevisiae etc.) via orthologs found by InParanoid program. Data of different sources and various natures, such as contacts of whole proteins and individual domains, mRNA and protein expression, localization in tissues and cellular compartments, miRNA and TF targeting, similar phylogenetic profiles etc. are collected and evaluated.
website/fungalgenomesize.html 0000644 0002441 0001757 00000002627 11606605737 016564 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Fungal genome size database
Fungal genome size database
website/funpep.html 0000644 0002441 0001757 00000002510 11606605737 014506 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FUNPEP information system for "low complexity sequence regions"
Information system for "low complexity sequence regions".
website/funshift.html 0000644 0002441 0001757 00000002403 11606605737 015040 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FunShift database
A compilation of function shift analysis performed between subfamilies in protein families.
website/funsimmat.html 0000644 0002441 0001757 00000003115 11606605737 015216 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FunSimMat database of semantic and functional similarity
A resource of semantic and functional similarity values. It allows searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB.
website/funybase.html 0000644 0002441 0001757 00000004065 11606605737 015034 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FUNYBASE fungal phylogenomic database
Database dedicated to the analysis of fungal proteins extracted from complete public fungal genomes, and their classification in clusters of orthologs.
website/fusiondb.html 0000644 0002441 0001757 00000002610 11606605737 015023 0 ustar jison industry
Bioinformatics Data Resource Catalogue
FusionDB database of bacterial and archaeal gene fusion events
A database of bacterial and archaeal gene fusion events.
website/g2cdb.html 0000644 0002441 0001757 00000002726 11606605737 014203 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Genes to cognition database (G2Cdb)
Genes to Cognition (G2C) is a neuroscience research programme that studies genes, the brain and behaviour in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition.
website/gabi-kat.html 0000644 0002441 0001757 00000002453 11606605740 014670 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GABI-Kat tags mutagenised A. thaliana
Generation of flanking sequence tags (FSTs) from T-DNA mutagenised A. thaliana plants.
website/gabipd.html 0000644 0002441 0001757 00000002716 11606605737 014447 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GabiPD: primary database of plant integrative biology
Primary database of plant integrative biology.
Example queries
| Data |
Format |
Query |
Example |
website/gbiffi.html 0000644 0002441 0001757 00000002317 11606605740 014436 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Global biodiversity information facility, Finland (GBIFFI)
Global biodiversity data.
website/gdb.html 0000644 0002441 0001757 00000002716 11606605740 013747 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GDB
Human Genome Database (GDB)
Community curated collection of human genomic data - now obsolete.
Example queries
| Data |
Format |
Query |
Example |
website/genatlas.html 0000644 0002441 0001757 00000006205 11606605740 015006 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GenAtlas human gene database
Information on gene apping and genetic diseases.
Available data
Example queries
website/genbank-dbsts.html 0000644 0002441 0001757 00000005755 11606605740 015743 0 ustar jison industry
Bioinformatics Data Resource Catalogue
STS database maintained at the NCBI (dbSTS)
An NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. All STS sequences are incorporated into the STS Division of GenBank.
Available data
Example queries
website/genbank.html 0000644 0002441 0001757 00000005502 11606605740 014614 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GenBank nucleotide sequence database
Nucleotide sequence database.
Available data
Example queries
website/gene3d.html 0000644 0002441 0001757 00000014460 11606605740 014357 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Gene3D structural and functional annotation of protein families
Gene3D structural and functional annotation of protein families incorporates several different sources including CATH, DRUGBANK, PFAM etc.
Available data
Example queries
website/geneannot.html 0000644 0002441 0001757 00000002601 11606605740 015162 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Affymetrix probe-sets database (GeneAnnot)
GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0.
website/genecards.html 0000644 0002441 0001757 00000022426 11606605740 015146 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GeneCards database of human genes, protein and diseases
GeneCards is a searchable, integrated database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs & compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents.
Available data
Example queries
website/genedb.html 0000644 0002441 0001757 00000005451 11606605740 014436 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GeneDB database from Sanger Institute Pathogen Sequencing Units
Sequence data and annotation/curation for the whole range of organisms sequenced by the PSU (Sanger Institute Pathogen Sequencing Units).
Available data
Example queries
website/genedb_spombe.html 0000644 0002441 0001757 00000007321 11606605740 016001 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Schizosaccharomyces pombe genome database (GeneDB_Spombe)
Sequence data and annotation/curation for Schizosaccharomyces pombe (fission yeast), including known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs.
Available data
Example queries
website/geneexpressiontooth.html 0000644 0002441 0001757 00000002413 11606605740 017321 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Gene expression in tooth database
Gene expression in tooth database
website/genefarm.html 0000644 0002441 0001757 00000010413 11606605740 014770 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GeneFarm annotation of Arabidopsis thaliana gene and protein families
Structural and functionnal annotation of plant gene and protein families by a network of experts.
Available data
Example queries
website/geneid.html 0000644 0002441 0001757 00000024407 11606605740 014447 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GeneID database of genes from NCBI RefSeq genomes
Database of genes from NCBI RefSeq genomes
Available data
Example queries
website/geneloc.html 0000644 0002441 0001757 00000003164 11606605740 014625 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GeneLoc map for human chromosomes
An integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources.
website/genenest.html 0000644 0002441 0001757 00000004146 11606605740 015022 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GeneNest transcript clusters
GeneNest is a comprehensive visualization of gene indices of various organisms. Each gene is represented by a single cluster of ESTs and/or mRNAs. Further subdivision of a cluster into contigs may be caused by alternative splicing, genomic sequences, or artefacts like chimeric sequences. Consensus sequence derived from GeneNest contigs are a basis for mapping genes onto the genome, and for analysis of splice isoforms.
website/genenote.html 0000644 0002441 0001757 00000003453 11606605740 015016 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GeneNote human genes and their expression profiles
A database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E.
website/genesapiens.html 0000644 0002441 0001757 00000002402 11606605740 015504 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GeneSapiens human transcriptome database
Human transcriptome database.
website/genesnps.html 0000644 0002441 0001757 00000005462 11606605740 015036 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SNPs Program at the University of Washington (GeneSNPs)
Gene-centric map of the genome structure, coding sequences, and identified allelic variation in genes being targeted for a role in disease susceptibility by the NIEHS (National Institute of Evironmental Health Sciences). This database provides a graphical view of all available SNP data including allele frequencies and genotypes in select populations. This information is key in selecting the polymorphic sites needed to examine disease risk in human population studies.
Available data
website/genetide.html 0000644 0002441 0001757 00000002511 11606605740 014770 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GeneTide database
An automated system for human transcripts (mRNA & ESTs) annotation and elucidation of de-novo genes.
website/genetree.html 0000644 0002441 0001757 00000005307 11606605740 015010 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GeneTree
GeneTree
Available data
Example queries
website/genevestigator.html 0000644 0002441 0001757 00000005411 11606605740 016234 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Genevestigator
Genevestigator
Available data
Example queries
website/genolevures.html 0000644 0002441 0001757 00000003235 11606605741 015547 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Genolevures 18 yeast genomes
Annotated sequence data and classifications for the genomes of eighteen species of hemiascomycete yeasts, including nine complete genomes.
website/genolist.html 0000644 0002441 0001757 00000011145 11606605741 015034 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GenoList comparative analysis of microbial genomes
An integrated environment for the analysis of microbial genomes.
Available data
Example queries
website/genomereviews.html 0000644 0002441 0001757 00000006077 11606605741 016077 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GenomeReviews database of completely sequenced genomes
Annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota.
Available data
Example queries
website/genomernai.html 0000644 0002441 0001757 00000002522 11606605741 015333 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GenomeRNAi database
Phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells.
website/genomicthreadingdatabase.html 0000644 0002441 0001757 00000002455 11606605741 020210 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Genomic threading database
Structural annotations of proteomes, translated from the genomes of key organisms.
website/germlinep53mutations.html 0000644 0002441 0001757 00000002467 11606605741 017315 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Germline p53 Mutations database
Germline p53 mutations
website/germonline.html 0000644 0002441 0001757 00000006022 11606605741 015345 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Gametogenesis and reproductive tissue expression
High-throughput expression data relevant for germline development and fertility across species.
Available data
Example queries
| Data |
Format |
Query |
Example |
website/glycatebase.html 0000644 0002441 0001757 00000002516 11606605741 015475 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GlycateBase glycation prediction
Glycation of amino groups of lysines in mammalian proteins.
website/glycomedb.html 0000644 0002441 0001757 00000002566 11606605741 015164 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Glycome database
Integrated database of carbohydrate structure and annotations, incorporating data from all freely available databases (CFG , KEGG, GLYCOSCIENCES.de, BCSDB and Carbbank).
website/glycosciencesdb.html 0000644 0002441 0001757 00000011522 11606605741 016347 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Glycosciences database
Carbohydrate structure database.
Available data
Example queries
website/glycosuitedb.html 0000644 0002441 0001757 00000005664 11606605741 015716 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GlycoSuiteDB glycan database
An annotated and curated relational database of glycan structures.
Available data
Example queries
website/goa.html 0000644 0002441 0001757 00000013544 11606605741 013763 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Gene ontology annotation database for UniProt (GOA-UniProt)
Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI).
Available data
Example queries
website/go.html 0000644 0002441 0001757 00000005474 11606605741 013625 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Gene ontology
Controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members. THe aim is to standardize representations of gene and gene product attributes across species and databases.
Available data
Example queries
website/golddb.html 0000644 0002441 0001757 00000003042 11606605741 014440 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GOLDDB database of genomics of lipid-associated disorders
GOLDDB integrates disparate information on the function and properties of genes and their protein products that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders including non-insulin dependent diabetes, various hyperlipidemias, high blood pressure and atherosclerosis.
website/gold.html 0000644 0002441 0001757 00000002374 11606605741 014141 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Genomes database
Information on complete and ongoing genome projects, as well as metagenomes and metadata.
website/gopubmed.html 0000644 0002441 0001757 00000002471 11606605741 015014 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GoPubMed ontology-based literature search
Ontology-based literature search.
website/gpcrdb.html 0000644 0002441 0001757 00000006125 11606605741 014453 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Information system for G protein-coupled receptors (GPCRs)
GPCR family profiles, mutation data (in various formats), ligand binding data, sequence annotations and cross-references to other databases.
Available data
Example queries
website/gpcr_nava.html 0000644 0002441 0001757 00000002446 11606605741 015154 0 ustar jison industry
Bioinformatics Data Resource Catalogue
GPCR natural variants database
Sequence variants within the family of human G Protein-Coupled Receptors (GPCRs).
website/gpdb.html 0000644 0002441 0001757 00000002751 11606605741 014127 0 ustar jison industry
Bioinformatics Data Resource Catalogue
A database of G-proteins,GPCRs,effectors and their interactions
Relational database of G-proteins and their interactions with GPCRs and effector molecules. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature search.
website/gramene.html 0000644 0002441 0001757 00000006640 11606605741 014632 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Gramene database for comparative grass genomics
Gramene adds value to public data sets of grass genomes and helps to compare, identify and understand genes, pathways and phenotypes from different grass species.
Available data
Example queries
website/greenphyldb.html 0000644 0002441 0001757 00000003550 11606605741 015514 0 ustar jison industry
Bioinformatics Data Resource Catalogue
A phylogenomic database for plant comparative genomics
Database for comparative genomic analyses of Arabidopsis thaliana and Oryza sativa full genomes.
website/grin.html 0000644 0002441 0001757 00000004116 11606605742 014150 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Germplasm Resources Information Network (GRIN)
GRIN taxonomic data provide the structure and nomenclature for accessions of the National Plant Germplasm System (NPGS). All families and genera of vascular plants and species from throughout the world are represented, especially economic plants and their relatives. Information on scientific and common names, classification, distribution, references, and economic impacts are provided.
Example queries
| Data |
Format |
Query |
Example |
website/gydb.html 0000644 0002441 0001757 00000002754 11606605742 014144 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Gypsy database of mobile genetic elements
Molecular diversity and evolutionary relationships of mobile genetic elements, viruses and related host genes.
website/haemb.html 0000644 0002441 0001757 00000002524 11606605742 014266 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Haemophilia B Mutation Database
Point mutations and short additions and deletions in the factor IX gene
website/hamap.html 0000644 0002441 0001757 00000014141 11606605742 014276 0 ustar jison industry
Bioinformatics Data Resource Catalogue
High-quality automated and manual annotation of microbial proteomes (HAMAP)
A system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
Available data
Example queries
website/hamasters.html 0000644 0002441 0001757 00000002503 11606605742 015176 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Haemophilia A FVIII mutation database (HAMASTERS)
Resources for Haemophilia A / factor VIII (FVIII) genetic variation at the DNA and protein level.
website/hcad.html 0000644 0002441 0001757 00000002415 11606605742 014110 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human chromosome aberration database (HCAD)
Human chromosome aberration database.
website/hepseq.html 0000644 0002441 0001757 00000002625 11606605742 014501 0 ustar jison industry
Bioinformatics Data Resource Catalogue
HepSeq international repository for Hepatitis B virus strain data
Molecular, clinical and epidemiological database for hepatitis B infection.
website/hervd.html 0000644 0002441 0001757 00000003113 11606605742 014315 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human endogenous retrovirus database (HERVd)
A database compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects, for screening human genome for HERVs. The HERV database now contains retroviruses from more than 90 % of the human genome.
website/hgdp-ceph.html 0000644 0002441 0001757 00000002504 11606605742 015047 0 ustar jison industry
Bioinformatics Data Resource Catalogue
HGDP-CEPH diversity panel database (HGDP-CEPH)
Polymorphic marker genotypes generated by users of the DNAs of the HGDP-CEPH Diversity Panel.
website/hgmd.html 0000644 0002441 0001757 00000002360 11606605742 014127 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human gene mutation database (HGMD)
Known (published) gene lesions responsible for human inherited disease.
website/hgnc.html 0000644 0002441 0001757 00000007222 11606605742 014131 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human gene nomenclature database (HGNC)
Database of unique and meaningful names for all human genes.
Available data
Example queries
website/hgt-db.html 0000644 0002441 0001757 00000003600 11606605742 014353 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Horizontal gene transfer-database (HGT-DB)
Genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer.
website/hgvbaseg2p.html 0000644 0002441 0001757 00000002547 11606605742 015247 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human Genome Variation database of Genotype-to-Phenotype information (HGVbaseG2P)
Centralized compilation of summary level findings from genetic association studies, both large and small.
website/hic-up.html 0000644 0002441 0001757 00000002254 11606605742 014377 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Hetero-compound information (HIC-Up)
Structural biology of hetero-compounds ("small molecules").
website/h-invdb.html 0000644 0002441 0001757 00000022771 11606605742 014547 0 ustar jison industry
Bioinformatics Data Resource Catalogue
H-InvDB integrated database of human genes and transcripts
From extensive analyses of all human transcripts, H-InvDB provides curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups.
Available data
Example queries
website/hmdb.html 0000644 0002441 0001757 00000003044 11606605743 014123 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human Metabolome Database (HMDB)
Information about small molecule metabolites found in the human body. It contains or links three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data.
website/hmtdb.html 0000644 0002441 0001757 00000002736 11606605742 014315 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human mitochondrial genomic database (HmtDB)
Human mitochondrial genomic database based on variability studies supporting population genetics and biomedical research.
website/hogenom.html 0000644 0002441 0001757 00000013556 11606605742 014655 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of homologous sequences from complete genomes (HOGENOM)
Homologous genes from fully sequenced organisms. It allows selection of sets of homologous genes among species, and visualisation of multiple alignments and phylogenetic trees. It is useful for comparative sequence analysis, phylogeny, molecular evolution studies and to get a view of what is known about a peculiar gene family.
Available data
Example queries
website/hoinvgen.html 0000644 0002441 0001757 00000004242 11606605742 015026 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Homologous invertebrate genes database (HOINVGEN)
Homologous invertebrate genes. It allows selection of sets of homologous genes among invertebrate species, and visualisation of multiple alignments and phylogenetic trees. It is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies or more generally, for an overall view of what is known about a peculiar gene family.
website/homeoboxpage.html 0000644 0002441 0001757 00000002534 11606605742 015670 0 ustar jison industry
Bioinformatics Data Resource Catalogue
HomeoboxPage homeobox gene page
Information relevant to homeobox genes, in particular about classification/evolution.
website/homomint.html 0000644 0002441 0001757 00000003103 11606605742 015036 0 ustar jison industry
Bioinformatics Data Resource Catalogue
HomoMINT inferred human protein interaction network
Database for extending protein-protein interactions experimentally verified in models organisms, to the orthologous proteins in Homo sapiens.
website/homstrad.html 0000644 0002441 0001757 00000003036 11606605743 015033 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Homologous structure alignment database (HOMSTRAD)
A curated database of annotated, structure-based sequence alignments for homologous protein families, from all known protein structure.
website/hoppsigen.html 0000644 0002441 0001757 00000002523 11606605743 015206 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Homologous processed pseudogenes database (Hoppsigen)
Nucleic database of homologous processed pseudogenes.
website/horde.html 0000644 0002441 0001757 00000003471 11606605743 014316 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human olfactory receptor data explorer (HORDE)
Database of human Olfactory Receptors (ORs), the largest multigene family in multicellular organisms. Information on the OR proteins, their gene structure and their genomic organization. Also available are OR repertoires of other mammalian species.
website/hotsprint.html 0000644 0002441 0001757 00000003003 11606605743 015236 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Computational Hot Spots of Protein Interfaces (HotSprint) database
Information about the evolutionary history of the residues on the interface and represents which residues are highly conserved on the interface. In this way, functionally and structurally important residues on the interface can be distinguished.
website/hovergen.html 0000644 0002441 0001757 00000013637 11606605742 015036 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Homologous vertebrate genes database (HOVERGEN)
Homologous vertebrate genes. It allows selection of sets of homologous genes among vertebrate species, and visualisation of multiple alignments and phylogenetic trees. It is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies or more generally, for an overall view of what is known about a peculiar gene family.
Available data
Example queries
website/hpa.html 0000644 0002441 0001757 00000013653 11606605743 013770 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human protein atlas (HPA) of expression and localization of proteins
Expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry (IHC) images and immunofluorescence (IF) confocal microscopy images.
Available data
Example queries
website/hs3d.html 0000644 0002441 0001757 00000003223 11606605743 014051 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Homo sapiens splice sites dataset (HS3D)
Homo Sapiens Exon, Intron and Splice regions extracted from GenBank.
website/hssp.html 0000644 0002441 0001757 00000005562 11606605743 014175 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Homology-derived secondary structure of proteins database (HSSP)
Homology-derived secondary structure of proteins database.
Available data
Example queries
website/htpselex.html 0000644 0002441 0001757 00000002645 11606605743 015053 0 ustar jison industry
Bioinformatics Data Resource Catalogue
HTPSELEX database of high-throughput SELEX libraries for transcription factor binding sites
Sets of invitro selected transcription factor binding site sequences obtained with SELEX and high-throughput SELEX method.
website/huge.html 0000644 0002441 0001757 00000006120 11606605743 014137 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human unidentified gene-encoded large proteins database (HUGE)
Database of the human cDNA project at the Kazusa DNA Research Institute, covering various sets of large human proteins of hitherto unidentified functions.
Available data
Example queries
website/humanmtdb.html 0000644 0002441 0001757 00000003065 11606605743 015173 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human mitochondrial genome database (HumanMtDB)
Human mitochondrial genome database.
website/humanpax6.html 0000644 0002441 0001757 00000002401 11606605743 015114 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human PAX6 allelic variant database (HumanPAX6)
Human PAX6 allelic variant database.
website/husida.html 0000644 0002441 0001757 00000002664 11606605743 014475 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human siRNA database
Depository for both sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments.
website/hvrbase++.html 0000644 0002441 0001757 00000002347 11606605743 014776 0 ustar jison industry
Bioinformatics Data Resource Catalogue
HvrBase++ phylogenetic database for primate species
Hypervariable regions database.
website/hypercat.html 0000644 0002441 0001757 00000003335 11606605743 015033 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Bacillus cereus group Typing Database (HyperCAT)
Typing databases for the Bacillus cereus group of bacteria, which includes B. cereus, B. anthracis, B. thuringiensis, B. mycoides, B. pseudomycoides, and B. weihenstephanensis. The databases contain MultiLocus Sequence Typing (MLST), MultiLocus Enzyme Electrophoresis (MLEE), and Amplified Fragment Length Polymorphism (AFLP) phylogenetic data.
website/hypercldb.html 0000644 0002441 0001757 00000002777 11606605743 015201 0 ustar jison industry
Bioinformatics Data Resource Catalogue
HyperCLDB cell line database
Cell culture availability extracted from the cell line database of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue and PubMed database of bibliographic biomedical references.
website/iarctp53.html 0000644 0002441 0001757 00000002514 11606605743 014644 0 ustar jison industry
Bioinformatics Data Resource Catalogue
IARC TP53 mutation database
All TP53 gene variations identified in human populations and tumor samples. Data are compiled from the peer-reviewed literature and from generalist databases.
website/icd.html 0000644 0002441 0001757 00000003033 11606605744 013747 0 ustar jison industry
Bioinformatics Data Resource Catalogue
International Classification of Diseases
The ICD is the international standard diagnostic classification of diseases for all general epidemiological, many health management purposes and clinical use. It is used to classify diseases and other health problems recorded on many types of health and vital records including death certificates and health records.
website/icds.html 0000644 0002441 0001757 00000002375 11606605744 014142 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Interrupted coding sequences (ICDS)
Interrupted coding sequences.
website/idbases-btkbase.html 0000644 0002441 0001757 00000006045 11606605743 016240 0 ustar jison industry
Bioinformatics Data Resource Catalogue
BTKbase database of X-linked agammaglobulinemia (XLA) mutations
Database of defects in the Bruton tyrosine kinase (BTK) gene causing agammaglobulinemia. Agammaglobulinemia is characterized by failure to produce mature B lymphocyte cells and is associated with a failure of Ig heavy chain rearrangement.
Available data
Example queries
website/idbases.html 0000644 0002441 0001757 00000006010 11606605743 014617 0 ustar jison industry
Bioinformatics Data Resource Catalogue
IDbases immunodeficiency mutation databases
Locus-specific databases for immunodeficiency-causing mutations.
Available data
Example queries
website/imgt_3dstructure-db.html 0000644 0002441 0001757 00000003106 11606605744 017103 0 ustar jison industry
Bioinformatics Data Resource Catalogue
IMGT 3D structure database for immunoglobulins (IG), T cell receptors (TR), MHC and RPI
IMGT 3D structure database for immunoglobulins (IG), T cell receptors (TR), MHC and RPI.
website/imgt_gene-db.html 0000644 0002441 0001757 00000003132 11606605744 015531 0 ustar jison industry
Bioinformatics Data Resource Catalogue
IMGT gene database for immunoglobulins (IG) and T cell recetors (TR)
IMGT gene database for immunoglobulins (IG) and T cell recetors (TR).
Example queries
| Data |
Format |
Query |
Example |
website/imgt_hla.html 0000644 0002441 0001757 00000006047 11606605743 015003 0 ustar jison industry
Bioinformatics Data Resource Catalogue
IMGT database of human MHC
A specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System.
Available data
Example queries
website/imgt.html 0000644 0002441 0001757 00000006034 11606605743 014153 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The international immunogenetics database (IMGT)
Database for the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species.
Available data
Example queries
website/imgt_ligm.html 0000644 0002441 0001757 00000003460 11606605744 015164 0 ustar jison industry
Bioinformatics Data Resource Catalogue
IMGT nucleotide sequence database for immunoglobulins (IG) and T cell recetors (TR)
IMGT nucleotide sequence database for immunoglobulins (IG) and T cell recetors (TR).
Example queries
| Data |
Format |
Query |
Example |
website/imgt_primer-db.html 0000644 0002441 0001757 00000003102 11606605744 016106 0 ustar jison industry
Bioinformatics Data Resource Catalogue
IMGT primer database for immunoglobulins (IG) and T cell recetors (TR)
IMGT primer database for immunoglobulins (IG) and T cell recetors (TR).
website/index.html 0000644 0002441 0001757 00000053472 11600347104 014316 0 ustar jison industry
Bioinformatics Data Resource Catalogue
DRCAT Resource Catalogue
Bioinformatics Web-based Data Resources
- Introduction
- Resource metadata
- Example entries
- Browse DRCAT
DRCAT (the data resource catalogue) collates metadata on bioinformatics Web-based data resources including databases, ontologies, taxonomies and catalogues. A DRCAT entry includes information such as resource identifier(s), name, description and URL. `Query' lines are defined for each resource that describe what type(s) of data are available, in what format, how (by what identifier) the data can be retrieved and from where (URL).
DRCAT was developed to provide more extensive data integration for EMBOSS, but it has many applications beyond EMBOSS. DRCAT entries (including 'Query' lines) are annotated with terms from the EDAM ontology of common bioinformatics concepts.
An "alpha" version is available:
http://sourceforge.net/projects/drcat/files/
It contains a comprehensive set of resourcs that are fully annotated and a starting point for 'Query' line definition. It includes:
- 655 entries
- 521 'Query' lines
- 2147 EDAM annotations
The "alpha" version is intended primarily to solicit feedback. DRCAT is being actively developed: contributions and suggestions are welcome. For further information contact Jon Ison (jison@ebi.ac.uk).
DRCAT can be viewed in any text editor. It can also be browsed.
DRCAT is made available to all without any constraint or license on its use or redistribution other than:
- DRCAT is clearly acknowledged as the source of the product
- DRCAT files displayed publicly include the publication date and/or version number
- DRCAT files are not altered and subsequently redistributed under their original name
All enquiries to Jon Ison (jison@ebi.ac.uk) cc'ing Peter Rice(pmr@ebi.ac.uk) and Matus Kalas (matus.kalas@bccs.uib.no)
Thanks to Peter Rice and Matus Kalas for valuable discussions and contributions.
Feel free to subscribe to one or both of the mailing lists:
Once subscribed, you can mail the lists:
drcat-developers is for technical discussions between EDAM developers / contributors. drcat-users is for general discussions and announcements. Traffic will be kept to a minimum.
Comment lines begin with '#' and can appear anywhere.
Resources might be cross-referenced from an EMBL or SwissProt entry. Database identifiers and names are taken (where available) from:
Note that SwissProt identifiers are listed in the the file dbxref.
ID <ID>
Recommended / official unique identifier.
e.g.
ID EcID
Value of <ID> is a string (no whitespace). A single ID line is given per entry.
IDalt <ID>
An alternative identifier.
e.g.
IDalt 2DBase-Ecoli
Value of <IDalt> is a string (no whitespace). Multiple IDalt lines may be given per entry (one IDalt / line).
Acc <Acc>
Accession number of database.
e.g.
Acc DB-0115
Value of <Acc> is a string (no whitespace).Values are taken from dbxref (if defined). A single Acc line only is given per entry.
Name <Text>
Verbose name.
e.g.
Name Structural classification of proteins (SCOP) database
Values are taken from dbxref (if defined) or otherwise are assigned. A single Name line only is given per entry.
Desc <Text>
Description of resource.
e.g.
Desc The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
Value of Text is any free text (but typically text from resource home page). A single Desc line only is given per entry.
URL <URL>
URL of resource server.
e.g.
URL http://scop.mrc-lmb.cam.ac.uk/scop
Value of <URL> is a resolvable URL. A single URL line only is given per entry.
URLlink
URL for instructions on how to link to the database.
e.g.
URLlink http://gene3d.biochem.ucl.ac.uk/Gene3D/linking
Value of <URLlink> is a resolvable URL. A single URLlink line only is given per entry.
URLrest
URL of documentation on REST-based interface (if available).
e.g.
URLrest http://www.ebi.ac.uk/pride/prideMartWebService.do
Value of <URLrest> is a resolvable URL. A single URLrest line only is given per entry.
URLsoap
URL of documentation on SOAP-based interface (if available).
e.g.
URLsoap http://api.cathdb.info/api/soap/dataservices/wsdl
Value of <URLsoap> is a resolvable URL. Single URLsoap line per entry.
Cat <Cat>
Database category.
e.g.
Cat 2D gel databases
Values taken from dbxref.txt (if defined).
A single Cat line only is given per entry.
Taxon <tax_id> | <scientific_name>
Annotation of the taxonomic scope of the resource.
e.g.
Taxon 562 | Escherichia coli
Values of <tax_id> and <scientific_name> are the taxonomic ID and scientific name of an organism taken from the NCBI Taxonomy. Multiple Taxon lines may be given.
EDAMdat <EDAM_id> | <EDAM_term>
EDAM annotation of the data returned by a query.
e.g.
EDAMdat 0001554 | SCOP node
Values of <EDAM_id> and <EDAM_term> are a unique identifier and term name for a concept from the EDAM ontology "Data" branch. Multiple EDAMdat lines may be given.
EDAMfmt <EDAM_id> | <EDAM_term>
EDAM annotation of the format of data returned by a query.
e.g.
EDAMfmt 0001929 | FASTA format
Values of <EDAM_id> and <EDAM_term> are a unique identifier and term name for a concept from the EDAM ontology "Format" branch. Multiple EDAMfmt lines may be given.
EDAMid <EDAM_id> | <EDAM_term>
EDAM annotation of the data identifier used as a query.
e.g.
EDAMid 0001033 | Gene ID (Ensembl)
Values of <EDAM_id> and <EDAM_term> are a unique identifier and term name for a concept from the EDAM ontology "Identifier" branch. Multiple EDAMid lines may be given.
EDAMtpc <EDAM_id> | <EDAM_term>
EDAM annotation of the resource itself.
e.g.
EDAMtpc 0000147 | Protein-protein interactions
Values of <EDAM_id> and <EDAM_term> are a unique identifier and term name for a concept from the EDAM ontology "Topic" branch. Multiple EDAMtpc lines may be given.
Xref <token> | <ID1;ID2>
Nature of cross-reference from a SwissProt or EMBL database entry.
e.g.
Xref SP_explicit | UniProt accession
Where <token> is one of:
- SP_explicit (explicit cross-reference from SP in database cross-reference (DR) line)
- SP_implicit (implicit cross-reference from SP in DR line)
- SP_CC (cross-reference from SP via URL address under the CC topic DATABASE)
- SP_FT (cross-reference from SP via key types in the feature table)
- SP_lit (cross-reference from SP to MedLine/PubMed stored in RX (Reference cross-reference) line)
- EMBL_DR (cross-reference from EMBL DR line)
- Other (some other type of reference)
- None (not cross-linked from SP or EMBL)
ID1, ID2 etc. give the type of identifier(s), i.e. term names from the EDAM "Identifier" branch, used in the cross-reference, e.g.
SP_explicit | EC number;OrganismID
Multiple Xref lines may be given. UniProt/SwissProt xrefs are described in detail in the UniProt userman.htm file.
SP_explicit
SP_explicit links are generally of the form:
DR database_name; primary_id; secondary_id
primary_id is usually an accession and secondary_id usually complements the first, e.g. entry name or version number.
SP_implicit
SP_implicit links are to databases that (typically) lack their own accession number scheme, but may be cross-referenced by 1) SP primary accession number or 2) some other identifier used by SP, e.g. gene name in the GN line. In both cases no extra DR line is present.
SP_CC
SP_CC links are to databases that (typically) are accessed via one URL, not by individual accessions.
SP_FT
SP_FTlinks are provided where the link concerns a feature.
SP_lit
SP_lit links the RX line provides the Medline or PubMed identifier.
Other
Other links include e.g. taxonomy identifier (Tax_id) that uniquely identifies an organism in NCBI taxonomy classification, and Enzyme EC numbers which are found in SP description (DE) lines.
Query <Data_type> {<comment>} | <Data_format> {<comment>} | <Data_identifier> {<comment>} | <URL>
Specification of data resource query.
e.g.
Query SCOP node | HTML | SCOP sunid | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=%s
Query Fungi annotation | HTML | Genus name;Species name | http://aftol.umn.edu/species/%s1_%s2
Query Fungi annotation (anamorph) | HTML | Genus name;Species name | http://aftol.umn.edu/species/%s1_%s2__(anamorph)
<Data_type>, <Data_format>, <Data_identifier> are term names from the EDAM ontology ("Data", "Format" and "Identifier" branches respectively). For each one, a corresponding EDAMdat, EDAMfmt or EDAMid annotation is given:
- <Data_type> is the type of data retrieved
- <Data_format> is the format of the data
- <Data_identifier> is the type of data identifier(s) (such as a sequence accession or EC number) that's used for query (in the URL component) and also in database cross-references (from SwissProt / EMBL).
- <URL> is used for data retrieval. %s in the URL should be replaced by an instance of the data identifier, e.g. a particular accession number.
Query lines may employ two or more data identifiers. In such cases identifiers are separated by a ';' and the URL should use %s1, %s2, %s3 etc (for first, second, third identifiers etc.). In the rare cases where the same ID is used twice in the URL then (e.g.) %s1 %s1 is used (for two uses of the first id) and %s2, %s3 etc (for second, third identifiers).
Multiple Query lines may be given. Note an optional comment may be given after <Datatype>, <Data_format> or <Data_identifier> and can be used for a provider-supplied names or comments for that type, format or identifier.
Example <Data_identifier> | <Example>
Example identifiers used in Query lines.
e.g.
Example Genus name | Aspergillus
Example Species name | giganteus
<Data_identifier> is a term name from the EDAM ontology ("Identifier" branch) as used in one or more Query lines. <Example> is valid value of the identifier for use in a query. Multiple Example lines may be given.
Example entries
ID AFTOL
Name Assembling the Fungal Tree of Life (AFTOL) database
Desc Fungal structural and biochemical database.
URL http://www.aftol.org/index.php
Cat Not available
Taxon 4751 | Fungi
EDAMtpc 0000782 | Fungal
EDAMid 0001045 | Species name
EDAMid 0001870 | Genus name
EDAMdat 0002395 | Fungi annotation
EDAMdat 0002396 | Fungi annotation (anamorph)
EDAMfmt 0002331 | HTML
Xref SP_FT | None
Query Fungi annotation | HTML | Genus name;Species name | http://aftol.umn.edu/species/%s1_%s2
Query Fungi annotation (anamorph) | HTML | Genus name;Species name | http://aftol.umn.edu/species/%s1_%s2__(anamorph)
Example Genus name | Aspergillus
Example Species name | giganteus
ID ANU-2DPAGE
Acc DB-0002
Name Australian National University 2-DE database (ANU-2DPAGE)
Desc 2-DE PAGE database.
URL http://semele.anu.edu.au
Cat 2D gel databases
Taxon 1 | all
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMid 0003021 | UniProt accession
EDAMdat 0002364 | Experiment annotation (2D PAGE)
EDAMfmt 0002331 | HTML
Xref SP_explicit | UniProt accession
Query Experiment annotation (2D PAGE) | HTML | UniProt accession | http://semele.anu.edu.au/cgi-bin/get-2d-entry?%s
Example UniProt accession | P02930
Example UniProt accession | Q9SIB9
ID SCOP
Name Structural classification of proteins (SCOP) database
Desc The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
URL http://scop.mrc-lmb.cam.ac.uk/scop
Taxon 1 | all
EDAMtpc 0000736 | Protein domains
EDAMdat 0001554 | SCOP node
EDAMdat 0002093 | Data reference
EDAMid 0001042 | SCOP sunid
EDAMid 0001127 | PDB ID
EDAMid 0000842 | Identifier
EDAMfmt 0002331 | HTML
Query SCOP node | HTML | SCOP sunid | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=%s
Query Data reference {PDB Entry search} | HTML | PDB ID | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?PDB=%s
Query Data reference | HTML | Identifier {Keyword} | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=%s
Example SCOP sunid | 47718
Example PDB ID | 1djh
Example Identifier {Keyword} | immunoglobulin
ID ECO2DBASE
IDalt 2DBase-Ecoli
IDalt EC-2D-GEL
Acc DB-0115
Name 2D-PAGE database of Escherichia coli
Desc This Database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins where identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analysed and compared in a tabular format based on varios functional categories enabling quick and subsequent analysis.
URL http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi
Cat 2D gel databases
Taxon 562 | Escherichia coli
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | Experiment annotation (2D PAGE)
EDAMid 0003021 | UniProt accession
EDAMfmt 0002331 | HTML
Xref SP_explicit | None
Query Experiment annotation (2D PAGE) {ECO2DBASE entry} | HTML | UniProt accession | http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?%s
Example UniProt accession | P02930
Example UniProt accession | P52697
ID Ensembl
Acc DB-0023
Name Ensembl eukaryotic genome annotation project
Desc Genome databases for vertebrates and other eukaryotic species.
URL http://www.ensembl.org/
Cat Genome annotation databases
Taxon 33208 | Metazoa
EDAMtpc 0000643 | Genomes
EDAMtpc 0002818 | Eukaryote
EDAMtpc 0000643 | Genomes
EDAMdat 0000849 | Sequence record
EDAMdat 0000916 | Gene annotation
EDAMid 0001033 | Gene ID (Ensembl)
EDAMid 0002725 | Transcript ID (Ensembl)
EDAMfmt 0001929 | FASTA format
EDAMfmt 0002331 | HTML
Xref SP_explicit | None
Xref SP_FT | None
Query Gene annotation | HTML | Gene ID (Ensembl) | http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=%s
Query Sequence record | FASTA format | Gene ID (Ensembl);Transcript ID (Ensembl) | http://www.ensembl.org/Homo_sapiens/Gene/Export?db=core;g=%s1;output=fasta;r=13:31787617-31871809;strand=feature;t=%s2;time=1244110856.85314;st=cdna;st=coding;st=peptide;st=utr5;st=utr3;st=exons;st=introns;genomic=unmasked;_format=Text
Example Gene ID (Ensembl);Transcript ID (Ensembl) | ENSG00000139618;ENST00000380152
website/infevers.html 0000644 0002441 0001757 00000002532 11606605744 015034 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Familial mediterranean fever (FMF) mutations database (INFEVERS)
The registry of familial mediterranean fever (FMF) and hereditary auto-inflammatory disorders mutations.
website/inparanoid.html 0000644 0002441 0001757 00000002457 11606605744 015345 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Inparanoid orthologs database
Eukaryotic orthholog groups.
website/intact.html 0000644 0002441 0001757 00000005602 11606605744 014476 0 ustar jison industry
Bioinformatics Data Resource Catalogue
IntAct protein interaction database and analysis system
Protein interaction database and analysis system.
Available data
Example queries
website/integr8.html 0000644 0002441 0001757 00000003420 11606605744 014570 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Integr8 genome and proteome database
Integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny.
website/integrall.html 0000644 0002441 0001757 00000002400 11606605744 015166 0 ustar jison industry
Bioinformatics Data Resource Catalogue
INTEGRALL integron integrases and gene cassettes
Database of DNA sequences and genetic arrangements.
website/intenz.html 0000644 0002441 0001757 00000003063 11606605744 014522 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Integrated relational enzyme database (IntEnz)
IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.
website/interpro.html 0000644 0002441 0001757 00000006370 11606605744 015061 0 ustar jison industry
Bioinformatics Data Resource Catalogue
InterPro integrated database of protein families, domains, regions, repeats and functional sites
Protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.
Available data
Example queries
website/ipd-estdab.html 0000644 0002441 0001757 00000003170 11606605744 015226 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Immuno polymorphism EST database (IPD-ESTDAB)
Searchable database of tumour cell lines.
website/ipd-hpa.html 0000644 0002441 0001757 00000002477 11606605744 014545 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Immuno polymorphism human platelet antigens database (IPD-HPA)
Information on human platelet antigens (HPA).
website/ipd.html 0000644 0002441 0001757 00000002654 11606605744 013774 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Immuno polymorphism database (IPD)
Database for the study of polymorphism in genes of the immune system.
website/ipd-kir.html 0000644 0002441 0001757 00000003307 11606605744 014553 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Immuno polymorphism killer-cell Immunoglobulin-like receptor database (IPD-KIR)
Sequences of human Killer-cell Immunoglobulin-like Receptors (KIR).
website/ipd-mhc.html 0000644 0002441 0001757 00000002504 11606605744 014533 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Immuno polymorphism major histocompatibility complex database (IPD-MHC)
Sequences of the the major histocompatibility complex in a number of species.
website/ipi.html 0000644 0002441 0001757 00000006200 11606605744 013770 0 ustar jison industry
Bioinformatics Data Resource Catalogue
International protein index (IPI)
Provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases.
Available data
Example queries
website/irefindex.html 0000644 0002441 0001757 00000003117 11606605744 015170 0 ustar jison industry
Bioinformatics Data Resource Catalogue
iRefIndex index of consolidated protein interactions
An index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods.
website/iresdb.html 0000644 0002441 0001757 00000002715 11606605744 014466 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Internal ribosome entry site database (IRESdb)
Internal ribosome entry sites.
website/iresite.html 0000644 0002441 0001757 00000003223 11606605744 014655 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of experimentally verified IRES structures (IRESite)
Information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.
website/isfinder.html 0000644 0002441 0001757 00000003216 11606605745 015017 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Insertion sequence elements database (ISfinder)
A database of insertion sequences isolated from eubacteria and archae. It is organised into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences.
Example queries
| Data |
Format |
Query |
Example |
website/isola.html 0000644 0002441 0001757 00000003042 11606605745 014320 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Italian Solanaceae genome resource (ISOLA)
Solanaceae genome resource.
website/its2.html 0000644 0002441 0001757 00000003346 11606605745 014101 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Internal transcribed spacer 2 sequences (ITS2)
Optimal global pairwise alignments from about 200,000 internal transcribed spacer 2 (ITS2) sequences - all against all - have been generated in order to model ITS2 secondary structures based on sequences with known structures.
website/ittaca.html 0000644 0002441 0001757 00000003366 11606605745 014467 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Integrated tumor transcriptome array and clinical data analysis (ITTACA)
Database created for Integrated Tumor Transcriptome Array and Clinical data Analysis. ITTACA centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular interest to the Institut Curie: breast carcinoma, bladder carcinoma, and uveal melanoma.
website/iupac.html 0000644 0002441 0001757 00000002303 11606605745 014311 0 ustar jison industry
Bioinformatics Data Resource Catalogue
IUPAC nomenclature database
Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology etc.
website/iuphar-db.html 0000644 0002441 0001757 00000002736 11606605745 015075 0 ustar jison industry
Bioinformatics Data Resource Catalogue
IUPHAR database
Official database of the IUPHAR Committee on Receptor Nomenclature and Drug Classification, incorporating the IUPHAR Database of G Protein-Coupled Receptors and the IUPHAR Database of Voltage-Gated and Ligand-Gated Ion Channels.
website/ixdb.html 0000644 0002441 0001757 00000002405 11606605745 014141 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Integrated X chromosome database (IXDB)
Integrated X chromosome database.
website/jail.html 0000644 0002441 0001757 00000003052 11606605745 014131 0 ustar jison industry
Bioinformatics Data Resource Catalogue
JAIL structure-based interface library for macromolecules
JAIL classifies not only the interfaces between domain architectures but also those between protein chains and those between proteins and nucleic acids.
website/jaspar.html 0000644 0002441 0001757 00000002720 11606605745 014473 0 ustar jison industry
Bioinformatics Data Resource Catalogue
JASPAR eukaryotic transcription factor binding profiles
High-quality transcription factor binding profile database.
website/jcm.html 0000644 0002441 0001757 00000003054 11606605745 013765 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Japan collection of microorganisms
Japan collection of microorganisms.
Example queries
| Data |
Format |
Query |
Example |
website/jenalib.html 0000644 0002441 0001757 00000003044 11606605745 014617 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Jena library of biological macromolecules (JenaLib)
Information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. JenaLib provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available.
website/jpgv.html 0000644 0002441 0001757 00000002345 11606605745 014164 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Jena prokaryotic genome viewer (JPGV)
Visualization and analysis of prokaryotic genomes.
website/jws.html 0000644 0002441 0001757 00000003001 11606605745 014007 0 ustar jison industry
Bioinformatics Data Resource Catalogue
JWS Online
JWS Online aims to provide a service to the Systems Biology community by 1) giving access to a database of curated models of biological systems, and 2) allowing the users to run these models in a web browser via an easy to use interface, and 3) helping in reviewing of manuscripts containing kinetic models.
website/karyotypedb.html 0000644 0002441 0001757 00000003075 11606605745 015554 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Karyotype features from different animals and plants
Karyotype and chromosome information like chromosome number, length, karyotype features, idiograms, physical localizations of DNA sequences by fluorescence in situ hybridizion (FISH), and cell material for metaphase chromosomes and polytene chromosomes from different animal and plant species together with literature references and links.
website/kdd.html 0000644 0002441 0001757 00000002512 11606605745 013754 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Kidney development database
Data from a large number of developmental studies that have a bearing on the study of kidney development.
website/kegg.html 0000644 0002441 0001757 00000012006 11606605745 014126 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Kyoto encyclopedia of genes and genomes (KEGG)
Encyclopedia of genes and genomes.
Available data
Example queries
website/kinmutbase.html 0000644 0002441 0001757 00000002524 11606605745 015357 0 ustar jison industry
Bioinformatics Data Resource Catalogue
KinMutBase registry of disease-causing mutations in protein kinase domains database
Disease-causing mutations in protein kinase domains.
website/kinomer.html 0000644 0002441 0001757 00000003314 11606605745 014657 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Kinomer database
A multilevel HMM library that models these protein kinase groups. It allows accurate identification of protein kinases and classification to the appropriate kinase group.
website/knottin.html 0000644 0002441 0001757 00000003140 11606605745 014676 0 ustar jison industry
Bioinformatics Data Resource Catalogue
KNOTTIN database
Database of knottins; intriguing miniproteins with strong potential in drug design.
website/l1base.html 0000644 0002441 0001757 00000002762 11606605745 014370 0 ustar jison industry
Bioinformatics Data Resource Catalogue
LINE-1 human and rodent
Putatively active LINE-1 (L1) insertions residing in human and rodent genomes: a) intact in the two ORFs, full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full length (>6000bp) non-intact L1s (FLnI-L1s) were also included.
website/leger.html 0000644 0002441 0001757 00000004054 11606605745 014313 0 ustar jison industry
Bioinformatics Data Resource Catalogue
LEGER genome database for Listeria research
LEGER links requirements of listerial research projects with knowledge derived from functional genome studies. LEGER provides information on gene functions, protein expression levels, subcellular localization of proteins and the biological meaning of genes and proteins based on KEGG, InterPro and Gene Ontology.
website/legiolist.html 0000644 0002441 0001757 00000010146 11606605746 015210 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Legionella pneumophila genome database
Legionella pneumophila genome database.
Available data
Example queries
website/leproma.html 0000644 0002441 0001757 00000010133 11606605746 014650 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Mycobacterium leprae genome database
Mycobacterium leprae genome database.
Available data
Example queries
website/lgicdb.html 0000644 0002441 0001757 00000010354 11606605746 014442 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ligand-gated ion channel database (LGICdb)
Nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available.
Available data
Example queries
website/ligasite.html 0000644 0002441 0001757 00000003024 11606605746 015013 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ligand attachment site database (LigAsite)
A gold-standard dataset of biologically relevant binding sites in protein structures.
website/lipaseengineering.html 0000644 0002441 0001757 00000002560 11606605746 016706 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Lipase engineering database
Integrates information on sequence and structure of lipases and related proteins sharing the same a/b hydrolase fold to facilitate protein engineering.
website/lipidbank.html 0000644 0002441 0001757 00000002430 11606605746 015147 0 ustar jison industry
Bioinformatics Data Resource Catalogue
LipidBank
A database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
website/lmsd.html 0000644 0002441 0001757 00000002457 11606605746 014162 0 ustar jison industry
Bioinformatics Data Resource Catalogue
LIPID MAPS Structure Database (LMSD)
Structures and annotations of biologically relevant lipids.
website/lumbribase.html 0000644 0002441 0001757 00000002754 11606605746 015350 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Lumbricus rubellus genome project database
Genome database for the earthworm, Lumbricus rubellus.
website/macie.html 0000644 0002441 0001757 00000002772 11606605746 014301 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Mechanism, annotation and classification in enzymes (MACiE) database
A database of enzyme reaction mechanisms, detailing the chemical compounds involved, individual reaction stages, mechanisms, alternative mechanisms, amino acids involved as well as the species name in which the reaction occurs.
website/maizegdb.html 0000644 0002441 0001757 00000006332 11606605746 015001 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Maize genetics and genomics database (MaizeGDB)
Biological information about the crop plant Zea mays ssp. mays. The following datatypes are accessible through this site: genetic, genomic, sequence, gene product, functional characterization, literature reference, and person/organization contact information.
Available data
Example queries
website/mamep.html 0000644 0002441 0001757 00000002456 11606605746 014321 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Molecular anatomy of mouse embryo project (MAMEP)
Functional analysis of pattern formation, tissue development and organogenesis in mouse.
website/mampol.html 0000644 0002441 0001757 00000002412 11606605746 014477 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Mammalia polymorphism database (MamPol)
A collection of all the existing polymorphic sequences in the Mammalia group.
website/mapu.html 0000644 0002441 0001757 00000002606 11606605746 014161 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Max-Planck unified proteome database (MAPU)
Body fluid proteomes including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth.
website/matdb.html 0000644 0002441 0001757 00000003145 11606605746 014305 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Arabadopsis genome database (MAtDB)
A repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project.
website/matrixdb.html 0000644 0002441 0001757 00000002365 11606605746 015033 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MatrixDB
A database of interactions established by extracellular proteins and polysaccharides.
website/medobis.html 0000644 0002441 0001757 00000002370 11606605746 014637 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Mediterranean ocean biogeographic information system (MedOBIS)
Regional repository of marine biodiversity data.
website/megx.html 0000644 0002441 0001757 00000002464 11606605746 014161 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MeGX marine microbial ecological genomics database
Specialized database for genome-wide analysis of marine bacteria and metagenomics.
website/mepd.html 0000644 0002441 0001757 00000002460 11606605746 014142 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Medaka expression pattern database (MEPD)
Medaka gene expression data examined through whole mount in situ hybridization.
website/merops.html 0000644 0002441 0001757 00000010301 11606605746 014513 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MEROPS peptidase database
Information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. Information includes the classification and nomenclature of the peptidase and links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.
Available data
Example queries
website/metacrop.html 0000644 0002441 0001757 00000003050 11606605746 015023 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MetaCrop database of metabolic pathways in crop plants
Diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models.
website/metagrowth.html 0000644 0002441 0001757 00000002544 11606605747 015402 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MetaGrowth database of culture conditions of obligate parasitic bacteria
Evidence and hypotheses for the study of culture conditions of obligate parasitic bacteria.
website/metal-macie.html 0000644 0002441 0001757 00000002645 11606605747 015401 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Metal-MACiE database of metals involved in biological catalysis
Properties and functions of the metal ions involved in the catalytic reactions of enzymes.
website/methdb.html 0000644 0002441 0001757 00000002313 11606605747 014456 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MethDB DNA methylation database
DNA methylation and environmental epigenetic effects.
website/mfungd.html 0000644 0002441 0001757 00000005673 11606605747 014507 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MIPS mouse functional genome database (MfunGD)
Mouse genome database including DNA and protein sequences, annotation, gene models and mapping etc.
Available data
Example queries
website/mgi.html 0000644 0002441 0001757 00000006616 11606605747 014001 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Mouse genome database (MGD) from Mouse Genome Informatics (MGI)
Integrated genetic, genomic, and biological data for mouse.
Available data
Example queries
website/micado.html 0000644 0002441 0001757 00000006366 11606605747 014463 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Microbial advanced database organisation (Micado)
Microbial genome and functional analysis of Bacillus subtilis.
Available data
Example queries
website/mim.html 0000644 0002441 0001757 00000006762 11606605747 014011 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Online Mendelian inheritance in Man (OMIM)
Compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype.
Available data
Example queries
website/mint.html 0000644 0002441 0001757 00000005517 11606605747 014173 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Molecular interaction Database (MINT)
Experimentally verified protein-protein interactions mined from the scientific literature by expert curators.
Available data
Example queries
website/mipsplantsdb.html 0000644 0002441 0001757 00000003473 11606605747 015723 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MIPS plants database
Data for individual plant species and a platform for integrative and comparative plant genome research.
website/mirbase.html 0000644 0002441 0001757 00000003070 11606605747 014636 0 ustar jison industry
Bioinformatics Data Resource Catalogue
miRBase database
Database of all published miRNA sequences, genomic locations and associated annotation, predicted miRNA target genes and a confidential service assigning official names for novel miRNA genes prior to publication of their discovery.
website/miriam.html 0000644 0002441 0001757 00000002476 11606605747 014503 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MIRIAM resources
Catalogue of data types (these can be controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources. Access to this data is made available via exports (XML) and Web Services (SOAP).
website/mirortho.html 0000644 0002441 0001757 00000002617 11606605747 015065 0 ustar jison industry
Bioinformatics Data Resource Catalogue
miROrtho animal microRNA database
Catalogue of animal microRNA genes.
website/mitodrome.html 0000644 0002441 0001757 00000004117 11606605747 015216 0 ustar jison industry
Bioinformatics Data Resource Catalogue
OXPHOS genes in Drosophila
Annotation for Drosophila melanogaster nuclear genes encoding for mitochondrial proteins in order to contribute to their functional characterization. The data collected in MitoDrome derive from the comparison of Human mitochondrial proteins available in SWISSPROT vs. the Drosophila genome, ESTs and cDNA sequences available in the FlyBase database. According to the results, each Drosophila gene sharing significant homology with a human mitochondrial protein was classified as a putative Drosophila mitochondrial gene and annotated in MitoDrome.
website/mitop2.html 0000644 0002441 0001757 00000003071 11606605747 014427 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Mitochondrial proteome database
Mitochondria-related genes, proteins and diseases.
website/mitores.html 0000644 0002441 0001757 00000002720 11606605747 014677 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MitoRes resource for mitochondria-related genes, transcripts and proteins
Mitochondria-related genes, transcripts and proteins
website/mlvabank.html 0000644 0002441 0001757 00000002347 11606605747 015015 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Bacterial MLVA-genotyping service (MLVAbank)
Bacterial MLVA-genotyping service.
website/mmdb.html 0000644 0002441 0001757 00000003060 11606605747 014132 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Molecular Modeling DataBase (MMDB)
A database of experimentally determined structures obtained from the RCSB Protein Data Bank (PDB). Useful features are added that facilitate computation on the data and link them to many other data types in the Entrez system.
website/mmmp.html 0000644 0002441 0001757 00000003730 11606605746 014164 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Melanoma Molecular Map Project (MMMP) i
A multidatabase dedicated to research on melanoma biology and therapy. It collects and integrates published data including melanoma-related molecular (or cellular) pathways of interest (Biomaps), structured and standardized information on single melanoma-related molecules of interest (Biocards), molecular derangements demonstrated in human melanoma (Melanoma Molecular Profile), preclinical and clinical information regarding drugs tested for melanoma treatment (Drug Development Database), Results form clinical trials (with therapeutic and/or, prognostic/predictive purposes), epidemiological studies, and meta-analyses (clinical Trial Database), key terms (or expressions, concepts) used in the MMMP site (Glossary).
website/mmruv.html 0000644 0002441 0001757 00000002605 11606605747 014365 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MMR Gene Unclassified Variants Database
Database of mismatch repair gene unclassified variants: information from functional assays and other type of data to support the interpretation of MMR gene unclassified variants.
website/mmsinc.html 0000644 0002441 0001757 00000002256 11606605747 014507 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MMsINC chemoinformatics database
Chemoinformatics database.
website/mncdb.html 0000644 0002441 0001757 00000003241 11606605750 014271 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MNCDB Neurospora crassa genome database
Molecular structure and functional network of the entirely sequenced, filamentous fungus Neurospora crassa.
website/modbase.html 0000644 0002441 0001757 00000012144 11606605750 014622 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ModBase database of comparative protein structure models
Three-dimensional protein models calculated by comparative modelling.
Available data
Example queries
website/modeldb.html 0000644 0002441 0001757 00000002343 11606605747 014624 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ModelDB
Computational neuroscience models.
website/modomics.html 0000644 0002441 0001757 00000002407 11606605750 015023 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of RNA modification pathways
Database of RNA modification pathways.
website/moka.html 0000644 0002441 0001757 00000003015 11606605750 014134 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MoKCa database of mutations of kinases in cancer
Structural and functional annotation on the phenotypic consequences of mutations in protein kinases implicated in cancer.
website/molligen.html 0000644 0002441 0001757 00000002406 11606605750 015016 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MolliGen Mollicutes database
Comparative genomics of Mollicutes.
website/monosaccharidedb.html 0000644 0002441 0001757 00000005227 11606605747 016507 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Monosaccharide database
Information on the residues used in glycan databases.
Available data
Example queries
website/mosaic.html 0000644 0002441 0001757 00000002422 11606605750 014461 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MOSAIC bacterial genome comparison database
Comparison of closely related bacterial genomes.
website/mosdb.html 0000644 0002441 0001757 00000003153 11606605750 014314 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MOsDB rice genome database
Publicly available sequences of the rice (Oryza sativa L.) genome.
website/mousebook.html 0000644 0002441 0001757 00000002640 11606605750 015213 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MouseBook data from MRC Harwell
All the data from MRC Harwell. This includes mouse stocks in FESA (Frozen Embryo and Sperm Archive), mutants from the mutagenesis screen, the ENU DNA archive, standardized phenotyping procedures, imprinting genes and chromosome anomalies.
website/mousesage.html 0000644 0002441 0001757 00000002772 11606605750 015206 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MouseSAGE serial analysis of gene expression database
Collection of public available SAGE libraries generated from various mouse tissues and cell lines. The libraries were collected from GEO repository as well as from individual laboratories that made the libraries freely available on the Internet or in their publications.
website/mpact.html 0000644 0002441 0001757 00000002464 11606605750 014320 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MPact: Representation of Interaction Data at MIP
Protein interaction resources from MIPS, designed to support the PSI-MI standard.
website/mtrdb.html 0000644 0002441 0001757 00000002364 11606605747 014331 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Microorganisms tandem repeats database
Microorganisms tandem repeats database.
website/mugen.html 0000644 0002441 0001757 00000002650 11606605750 014324 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MUGEN mouse database
Database of murine models of immune processes and immunological diseases.
website/mumdb.html 0000644 0002441 0001757 00000003236 11606605750 014316 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MIPS Ustilago maydis Database (MUMDB)
Molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis.
website/myhits.html 0000644 0002441 0001757 00000003762 11606605750 014533 0 ustar jison industry
Bioinformatics Data Resource Catalogue
MyHits protein domains database
Protein domain database for investigating the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models.
website/naproc-13.html 0000644 0002441 0001757 00000002542 11606605750 014714 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NAPROC-13 natural products 13C NMR database
Natural products 13C NMR, for the dereplication of natural product mixtures in bioassay-guided protocols.
website/narcisse.html 0000644 0002441 0001757 00000002401 11606605750 015012 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Narcisse mirror view of conserved synteny
Mirror view of conserved synteny.
website/nbrc.html 0000644 0002441 0001757 00000002562 11606605750 014137 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NITE biological resource center
Microbial culture catalogue.
website/ncl.html 0000644 0002441 0001757 00000002773 11606605750 013773 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NCL Mutation Database
Published mutations and polymorphisms in the NCL genes together with unpublished data included with permission.
website/ncrnas.html 0000644 0002441 0001757 00000002750 11606605750 014476 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ncRNAs database
Sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell.
website/nembase.html 0000644 0002441 0001757 00000002436 11606605750 014625 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NEMBASE database for analysis of nematode ESTs
Nematode EST datasets.
website/nesbase.html 0000644 0002441 0001757 00000002615 11606605750 014632 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NESbase database of leucine-rich nuclear export signals
Database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified. It is curated from literature.
website/neuromorpho.html 0000644 0002441 0001757 00000002565 11606605750 015573 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NeuroMorpho
NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons and associated metadata from peer-reviewed publications.
website/neurondb.html 0000644 0002441 0001757 00000003104 11606605751 015021 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NeuronDB
NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.
website/nextbio.html 0000644 0002441 0001757 00000006641 11606605751 014666 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NextBio gene-centric data for human, mouse, rat, fly, worm and yeast
NextBio gene-centric data for human, mouse, rat, fly, worm and yeast
Available data
Example queries
website/nextdb.html 0000644 0002441 0001757 00000003050 11606605751 014471 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Nematode expression pattern dataBase (NextDB)
Nematode expression pattern dataBase.
Example queries
| Data |
Format |
Query |
Example |
website/nextprot.html 0000644 0002441 0001757 00000005353 11606605751 015100 0 ustar jison industry
Bioinformatics Data Resource Catalogue
neXtProt; the human protein knowledge platform
neXtProt; the human protein knowledge platform
Available data
Example queries
website/niaest.html 0000644 0002441 0001757 00000002775 11606605751 014505 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NIA mouse cDNA project
NIA mouse cDNA project
Example queries
| Data |
Format |
Query |
Example |
website/nmpdr.html 0000644 0002441 0001757 00000011735 11606605751 014336 0 ustar jison industry
Bioinformatics Data Resource Catalogue
National microbial pathogen
Curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.
Available data
Example queries
website/nmrshift.html 0000644 0002441 0001757 00000002623 11606605751 015044 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NMRShift database of organic structure NMR spectra
An NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. It features peer-reviewed submission of datasets by its users.
website/nopdb.html 0000644 0002441 0001757 00000002630 11606605751 014312 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Nucleolar proteome database (NOPDB)
Data from LamondLab proteomic analysis of human nucleoli. High sensitivity mass spectrometry and stringent criteria is used to identify peptides from human proteins from purified nucleoli.
website/norine.html 0000644 0002441 0001757 00000002364 11606605751 014506 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NORINE database of nonribosomal peptides
Database of nonribosomal peptides.
website/npc-db.html 0000644 0002441 0001757 00000002341 11606605751 014352 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Niemann-Pick Type C mutations
Niemann-Pick type C disease gene variation database (NPC-db).
website/npd.html 0000644 0002441 0001757 00000003221 11606605751 013766 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Nuclear protein database (NPD)
Information on vertebrate proteins (mainly those from mouse and human) that are thought to, or known to, be localised to the cell nucleus. Where known, the sub-nuclear compartment where the proteins have been found are reported. Also stored is information on the amino acid sequence, predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. Biological and molecular functions of the proteins are described using GO terms.
website/nrestdb.html 0000644 0002441 0001757 00000003023 11606605751 014646 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Natural rubber EST database (NRESTdb)
Natural rubber EST database.
Example queries
| Data |
Format |
Query |
Example |
website/nrsub.html 0000644 0002441 0001757 00000002760 11606605751 014345 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Non-Redundant B.subtilis database (NRSub)
Complete genome of Bacillus subtilis, plus additional data on gene mapping and codon usage.
website/nurebase.html 0000644 0002441 0001757 00000002475 11606605751 015023 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Nuclear receptor database (NUREBASE)
Nuclear receptor database
website/oglycbase.html 0000644 0002441 0001757 00000003537 11606605751 015167 0 ustar jison industry
Bioinformatics Data Resource Catalogue
O-GlycBase database
Database of O- and C-glycosylated proteins. The criteria for inclusion are at least one experimentally verified O- or C-glycosylation site. The terminal sugar linked to serine or threonine is cited when known. The database is non-redundant in the sense that it contains no identical sequences, unless there is conflicting glycosylation data. Mucins have tandem repeat sequences, which are O-glycosylated. This result in some redundancy of the O-glycosylation sites.
website/ogp.html 0000644 0002441 0001757 00000005612 11606605751 014000 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Oxford glycoProteomics 2-DE database (OGP)
Two-dimensional polyacrylamide gel electrophoresis database.
Available data
Example queries
website/oma.html 0000644 0002441 0001757 00000006205 11606605751 013766 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Identification of orthologs from complete genome data (OMA database)
Identification of orthologs from complete genome data.
Available data
Example queries
website/optic.html 0000644 0002441 0001757 00000002574 11606605751 014335 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Orthologous and paralogous transcripts in clades (OPTIC) database
Orthologous and paralogous transcripts in clades, from anaylsis of complete genomes (flies, nematodes, amniota, yeasts) in several clades.
website/orenza.html 0000644 0002441 0001757 00000002436 11606605751 014512 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of orphan enzyme activities (ORENZA)
Enzyme Activities for which no sequences are available in the main sequence protein databases.
website/orphanet.html 0000644 0002441 0001757 00000006065 11606605751 015036 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Orphanet portal for rare diseases and orphan drugs
Information on rare diseases and orphan drugs.
Available data
Example queries
website/orthodb.html 0000644 0002441 0001757 00000002745 11606605751 014660 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Orthologous groups database (OrthoDB)
Orthologous groups database.
website/orygenesdb.html 0000644 0002441 0001757 00000003412 11606605751 015350 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database for rice reverse genetics (OryGenesDB)
Oryza sativa database of sequence information, such as the T-DNA and Ds flanking sequence tags (FSTs), plus related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data etc).
website/oryza.html 0000644 0002441 0001757 00000003432 11606605752 014356 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Oryza tag line
Database for the functional analyis of the rice genome. Phenotypic data from evaluation of the Genoplante rice insertion line library. Sequence information (Flanking Sequence Tags) from the molecular characterization of the mutagen insertion sites.
website/osteogenesis.html 0000644 0002441 0001757 00000013635 11606605752 015727 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Osteogenesis imperfecta and type III collagen mutations
All published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP and LEPRE1 genes.
Available data
Example queries
website/p53famtag.html 0000644 0002441 0001757 00000003011 11606605752 014772 0 ustar jison industry
Bioinformatics Data Resource Catalogue
p53FamTaG direct target genes
A resource of human p53, p63, p73 direct target genes combining in silico prediction and microarray analysis.
website/pairsdb.html 0000644 0002441 0001757 00000002606 11606605752 014640 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PairsDB BLAST and PSI-BLAST alignments
Collection of protein sequences and the BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually, results can be retrieved from a database of pre-computed alignments.
website/pandit.html 0000644 0002441 0001757 00000002514 11606605752 014471 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Protein and associated nucleotide domains with inferred trees (PANDIT)
Protein and associated nucleotide domains with inferred trees.
website/pandora.html 0000644 0002441 0001757 00000002443 11606605752 014637 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PANDORA visualization and annotation for protein sets
Keyword-based analysis of protein sets by integration of annotation sources.
website/panther.html 0000644 0002441 0001757 00000012241 11606605752 014651 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Protein analysis through evolutionary relationships (PANTHER)
Classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified by expert biologists into families and subfamilies of shared function, which are then categorized by molecular function and biological process ontology terms. PANTHER includes "PANTHER Genes" (genes, transcripts and proteins in Human, Mouse, Rat, and Drosophila melanogaster), PANTHER Families (Protein families and subfamilies and associated data such as phylogenetic trees, multiple sequence alignments and HMMs), "PANTHER Pathways" (expert-curated signaling and metabolic pathways mapped to protein sequences in PANTHER Library) and "PANTHER Ontologies".
Available data
Example queries
website/parameciumdb.html 0000644 0002441 0001757 00000003123 11606605752 015640 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database for the model organism Paramecium tetraurelia (ParameciumDB)
Macronuclear genome sequence and annotations, linked to available genetic data (RNA interference data and stock collection) for the model organism, Paramecium tetraurelia.
website/pathema.html 0000644 0002441 0001757 00000003550 11606605752 014632 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Pathema: a clade-specific bioinformatics resource
Genome database for six clades of Category A-C pathogens — Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica.
website/pathoplant.html 0000644 0002441 0001757 00000004214 11606605752 015363 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PathoPlant database of plant-pathogen interactions and Arabidopsis expression
Plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. Also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.
website/pathway_interaction_db.html 0000644 0002441 0001757 00000005735 11606605752 017743 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NCI-Nature pathway interaction database
Biomolecular interactions and cellular processes assembled into human signaling pathways.
Available data
Example queries
website/pdbe.html 0000644 0002441 0001757 00000002335 11606605752 014125 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PDBe protein structure database in Europe
PDBe protein structure database in Europe
website/pdbfinder.html 0000644 0002441 0001757 00000006360 11606605752 015152 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PDBFINDER reformatted PDB files
The PDBFINDER holds for each PDB file a structured, search-engine-friendly-formatted entry that holds the data-items most likely needed for people search for certain types of PDB entries. The PDBFINDER is not useful to search in atomic coordinates: it is meant to ad searches in the administrative records of PDB files.
Available data
Example queries
website/pdbfun.html 0000644 0002441 0001757 00000002353 11606605752 014471 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PDBfun annotated protein structures
Database of annotated residues in proteins from PDB.
website/pdb.html 0000644 0002441 0001757 00000012525 11606605752 013762 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The RCSB Protein Data Bank
A repository for 3D biological macromolecular structure data.
Available data
Example queries
website/pdb-redo.html 0000644 0002441 0001757 00000004625 11606605752 014713 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PDB-redo database of re-refined PDB entries
Re-refined macromolecular X-ray diffraction structures.
Available data
website/pdbreport.html 0000644 0002441 0001757 00000002642 11606605752 015215 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Structure validation reports for PDB entries (PDBREPORT)
Reports describing structural problems in PDB entries that have been determined using X-ray diffraction or NMR techniques. There are many more than ten million diagnostics.
website/pdbselect.html 0000644 0002441 0001757 00000002465 11606605752 015164 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PDBselect database of representative PDB chains
Selection of a representative set of PDB chains.
website/pdbsum.html 0000644 0002441 0001757 00000005646 11606605752 014515 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PDBsum overview of macromolecular structures
At-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
Available data
Example queries
website/pdbtm.html 0000644 0002441 0001757 00000002356 11606605752 014324 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Transmembrane proteins from PDB (PDBTM)
Transmembrane protein selection of the Protein Data Bank (PDB).
website/pedant.html 0000644 0002441 0001757 00000003746 11606605753 014476 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PEDANT3 protein extraction, description and analysis tool
Automatic analysis of genomic sequences by a large variety of bioinformatics tools. For example the following pre-computed analyses are available to analyse protein function: Blast similarity searches against the non-redundant protein sequence database, motif searches against the Pfam, BLOCKS and PROSITE databases. Prediction of cellular roles and functions are made based on high stringency BLAST searches against protein sequences with manually assigned functional categories according to the Functional Catalogue (FunCat) developed by MIPS and Biomax AG. Protein structure analysis includes the similarity-based identification of known 3D structures and structural domains, by searching against the PDB and SCOP databases, and predictions of transmembrane regions, low similarity regions and non-globular domains.
website/ped.html 0000644 0002441 0001757 00000003107 11606605753 013762 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Pancreatic expression database (PED)
Database for cancer pathogenesis, allowing query by cancer tissue and type, a wide range of sequence types, SNP selection for candidate gene screening and disease links, as well as cross-species analyses.
website/pepseeker.html 0000644 0002441 0001757 00000002627 11606605753 015203 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PepSeeker database of proteome peptide identifications for investigating fragmentation patterns
Proteome peptide identifications for investigating fragmentation patterns.
website/peptaibol.html 0000644 0002441 0001757 00000002634 11606605753 015175 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Peptaibol database of natural fungal peptides
Natural fungal peptides.
website/peptideatlas.html 0000644 0002441 0001757 00000023575 11606605753 015704 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PeptideAtlas peptide database
A multi-organism compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences.
Available data
Example queries
website/peptidedb.html 0000644 0002441 0001757 00000003171 11606605753 015153 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PeptideDB database of bioactive signaling peptides
Naturally occurring signalling peptides from animal source, which are derived by cleavage from prepropeptide precursor proteins. It includes cytokine and growth factor, peptide hormones, antimicrobial peptides, toxins and venom peptides, and antifreeze proteins.
website/peroxibase.html 0000644 0002441 0001757 00000005637 11606605753 015365 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PeroxiBase peroxidase family database
Sequences from peroxidase superfamilies with annotation on putative functions and transcription regulation.
Available data
Example queries
website/peroxisomedb.html 0000644 0002441 0001757 00000003504 11606605753 015713 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Peroxisome database (PeroxisomeDB)
Curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders. PeroxisomeDB contains the complete peroxisomal proteome of Homo sapiens (encoded by 85 genes) and Saccaromyces cerevisiae (encoded by 61 genes).
website/pespotdb.html 0000644 0002441 0001757 00000002567 11606605753 015043 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Pepspot database (PespotDB) of peptide chip data
Repository for the storage and the analysis of data coming from interaction assays exploiting peptide chip technology.
website/pfam.html 0000644 0002441 0001757 00000014347 11606605753 014145 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Pfam protein domain database
Large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
Available data
Example queries
website/pgn.html 0000644 0002441 0001757 00000003173 11606605753 014001 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Plant Genome Network (PGN)
A general purpose EST analysis pipeline/website that can be readily used as a "front end" for EST sequencing projects. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database.
website/pharmgkb.html 0000644 0002441 0001757 00000006732 11606605753 015014 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)
Database on the impact of human genetic variations on drug response. PharmGKB curates primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways.
Available data
Example queries
website/phci-2dpage.html 0000644 0002441 0001757 00000005527 11606605753 015305 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Parasite host cell interaction 2D-PAGE database (PHCI-2DPAGE)
Two-dimensional polyacrylamide gel electrophoresis database.
Available data
Example queries
website/phenomicdb.html 0000644 0002441 0001757 00000003016 11606605753 015321 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PhenomicDB cross-species genotype/phenotype database
A multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indexes (NCBI Gene) and orthologues (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously.
website/phi-base.html 0000644 0002441 0001757 00000003040 11606605753 014676 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PHI-base pathogen host interactions database
Curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. Information is also given on the target sites of some anti-infective chemistries.
website/phosphat.html 0000644 0002441 0001757 00000004012 11606605753 015034 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Arabidopsis experimental phosphorylation sites database (PhosPhAt)
Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups. Specific information on the peptide properties as well as on the experimental and analytical context is given.
website/phospho3d.html 0000644 0002441 0001757 00000003437 11606605753 015127 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PHOSPHO3D structures of phosphorylation sites
Three-dimensional structures of phosphorylation sites which stores information retrieved from the phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database also collects the results of a large-scale structural comparison procedure providing clues for the identification of new putative phosphorylation sites.
website/phosphoelm.html 0000644 0002441 0001757 00000010445 11606605753 015373 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PhosphoELM database of S/T/Y phosphorylation sites
Experimentally verified phosphorylation sites in eukaryotic proteins.
Available data
Example queries
website/phosphopep.html 0000644 0002441 0001757 00000002635 11606605753 015404 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PhosphoPep database of MS-derived phosphorylation data from 4 organisms
MS-derived phosphorylation data from 4 different organisms: the fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae).
website/phosphosite.html 0000644 0002441 0001757 00000006103 11606605753 015556 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Phosphorylation site database
A curated, sequence-oriented protein database dedicated to in vivo phosphorylation sites. Information in PhosphoSite version 1.0 includes the phosphorylated residue and its surrounding sequence, orthologous sites in other species, the location within domains and motifs, links to other online resources and literature references.
Available data
Example queries
website/phossite.html 0000644 0002441 0001757 00000005763 11606605753 015062 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Phosphorylation site database for Archaea and Bacteria
Phosphorylation site database for Archaea and Bacteria
Available data
Example queries
website/phylomedb.html 0000644 0002441 0001757 00000003250 11606605754 015175 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PhylomeDB database of phylogenetic trees for all proteins
A collection of gene phylogenies (phylomes) including phylogenetic trees, multiple sequence alignments and genome-wide orthology and paralogy predictions based on the analysis of the phylogenetic trees.
website/phylopat.html 0000644 0002441 0001757 00000002673 11606605754 015062 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PhyloPat database of phylogenetic patterns
Database for the analysis of where in evolution some phylogenetic lineages were started and over which species they were contained. PhyloPat uses the latest release of EnsMartand their one-to-one, one-to-many and many-to-many orthologies.
website/phytoprot.html 0000644 0002441 0001757 00000003173 11606605754 015266 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PhytoProt protein clusters database
Database built from "all-by-all" comparison of (putative) protein sequences and sequence clustering. Relationships between sequences in a cluster and help identify annotation errors (fused genes, missing exons, frameshifts, etc).
website/pips.html 0000644 0002441 0001757 00000002454 11606605754 014172 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Human protein-protein interaction prediction (PIPs)
Predicted human protein interactions.
website/pir.html 0000644 0002441 0001757 00000005535 11606605754 014014 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Protein sequence database of the Protein Information Resource (PIR)
Integrated protein informatics resource for genomic, proteomic and systems biology research.
Available data
Example queries
website/pirsf.html 0000644 0002441 0001757 00000006426 11606605754 014345 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PIRSF whole-protein classification database
Non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains.
Available data
Example queries
website/plantcare.html 0000644 0002441 0001757 00000003445 11606605754 015171 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Plant cis acting element
A database of different names of plant transcription sites (monocots, dicots and other) describing plant promoters, with plant transcription sites, consensus sequences and matrices.
website/plantdnac-values.html 0000644 0002441 0001757 00000003260 11606605754 016454 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Plant DNA C-values database (PlantDNAC-values)
The DNA amount in the unreplicated gametic nucleus of an organism is referred to as its C-value, irrespective of the ploidy level of the taxon. The Plant DNA C-values Database currently contains data for different plant species. It combines data from the Angiosperm DNA C-values Database, Gymnosperm DNA C-values Database, the Pteridophyte DNA C-values Database, the Bryophyte DNA C-values Database, together with the addition of the Algae DNA C-values database.
website/plantmarkers.html 0000644 0002441 0001757 00000002657 11606605754 015727 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PlantMarkers database of predicted molecular markers from plants
Predicted molecular markers from plants.
website/plant-pis.html 0000644 0002441 0001757 00000003037 11606605754 015124 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PLANT-Pis database for protease inhibitors and their genes in higher plants
Information on the distribution and functional properties of protease inhibitors (PIs) in higher plants.
website/plantprom.html 0000644 0002441 0001757 00000003517 11606605754 015234 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PlantProm database of experimental plant promoter and transcription start site
An annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species.
website/plantsnorna.html 0000644 0002441 0001757 00000002701 11606605754 015551 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Plant snoRNA database
Plant snoRNA database.
website/plasmodraft.html 0000644 0002441 0001757 00000003407 11606605754 015532 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Predictions of Plasmodium falciparum gene function
Gene Ontology (GO) annotation predictions for the genes of Plasmodium falciparum. It involves both the ~60% of genes that lake GO annotation, and the genes that are already annotated in GeneDB. Predictions of PlasmoDraft are based on transcriptome, proteome, and interactome data, and are thus complementary to predictions achieved by sequence homology.
website/plmitrna.html 0000644 0002441 0001757 00000003441 11606605754 015042 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PLMItRNA database of tRNAs in plant mitochondria
A database for tRNA molecules and genes in mitochondria of photosynthetic eukaryotes.
website/plprot.html 0000644 0002441 0001757 00000003534 11606605754 014537 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Plastid proteins database (Plprot)
Integrates data from large scale proteome analyses of different plastid types. These include etioplasts, chloroplasts, chromoplasts and the undifferentiated proplastid-like organelles of tobacco BY2 cells. This comparison yields a core proteome common to all plastid types and provides furthermore information about plastid type-specific functions.
website/pmap-cutdb.html 0000644 0002441 0001757 00000005375 11606605754 015260 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PMAP-CutDB proteolytic event database
Curated proteolytic events and pathways from the literature.
Available data
Example queries
website/pmdb.html 0000644 0002441 0001757 00000002541 11606605754 014136 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Protein model database (PMDB)
Three dimensional protein models from structure prediction methods. The database currently stores all models submitted to the last four editions of the CASP experiment.
website/pmma-2dpage.html 0000644 0002441 0001757 00000005513 11606605756 015312 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Purkyne Military Medical Academy 2D-PAGE database
Purkyne Military Medical Academy 2D-PAGE database
Available data
Example queries
website/polymorphix.html 0000644 0002441 0001757 00000002502 11606605754 015603 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Polymorphix intraspecific sequence polymorphism database
Families of polymorphic sequences.
website/pomamo.html 0000644 0002441 0001757 00000002364 11606605754 014507 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PoMaMo potato maps database
Potato sequences, mapping info, SNPs etc.
website/ppd.html 0000644 0002441 0001757 00000002414 11606605754 013776 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PPD protein pKa values database
Protein pKa values.
website/ppnema.html 0000644 0002441 0001757 00000002654 11606605754 014501 0 ustar jison industry
Bioinformatics Data Resource Catalogue
rRNA genes from plant-parasitic nematodes (PPNEMA)
Plant-parasitic nematodes multialigned ribosomal cistrons.
website/pptasedb.html 0000644 0002441 0001757 00000005563 11606605754 015025 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Prokaryotic protein phosphatase database (PptaseDB)
Prokaryotic protein phosphatases.
Available data
Example queries
website/predict.html 0000644 0002441 0001757 00000002356 11606605755 014653 0 ustar jison industry
Bioinformatics Data Resource Catalogue
preDiCT database of drug effects on the heart
Drug effects on the heart.
website/pride.html 0000644 0002441 0001757 00000006602 11606605755 014322 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PRIDE proteomics identifications database
Standards compliant, public data repository for proteomics data, protein and peptide identifications together with the evidence supporting these identifications.
Available data
Example queries
website/prints.html 0000644 0002441 0001757 00000006624 11606605755 014542 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PRINTS protein motif fingerprint database
A compendium of protein fingerprints, or group of conserved motifs used to characterise a protein family.
Available data
Example queries
website/prism.html 0000644 0002441 0001757 00000002465 11606605755 014354 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Prism protein interaction by structural matching
Database to explore protein interfaces and predict protein-protein interactions.
website/probebase.html 0000644 0002441 0001757 00000002720 11606605755 015156 0 ustar jison industry
Bioinformatics Data Resource Catalogue
probeBase database of rRNA-targeted oligonucleotide probes
rRNA-targeted oligonucleotide probes.
website/procmd.html 0000644 0002441 0001757 00000003442 11606605755 014502 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ProCMD 3D protein C mutations database
Database for molecular aspects of thrombophilic disease. It integrates clinical and phenotypical descriptions with functional and structural data obtained by computational approach to help to elucidate the chain of events leading from the molecular defect to disease.
website/procognate.html 0000644 0002441 0001757 00000004225 11606605755 015357 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PROCOGNATE ligand domain mapping for enzymes
Cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam. The database contains an assignment of PDB ligands to the domains of structures as classified by the CATH, SCOP and Pfam databases. Cognate ligands have been identified using data from the ENZYME and KEGG databases and compared to the PDB ligand using graph matching to assess chemical similarity. Cognate ligands from the known reactions in ENZYME and KEGG for a particular enzyme are then assigned to enzymes structures which have EC numbers.
website/prodom.html 0000644 0002441 0001757 00000016605 11606605755 014523 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ProDom protein domain database
A comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.
Available data
Example queries
website/prodoric.html 0000644 0002441 0001757 00000003070 11606605755 015034 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PRODORIC prokaryotic database of gene regulation
Comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.
website/promec.html 0000644 0002441 0001757 00000002740 11606605755 014503 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PromEC verified E. coli promoters
E. coli mRNA promoters with experimentally identified transcriptional start sites.
website/promex.html 0000644 0002441 0001757 00000007341 11606605755 014532 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ProMEX protein mass spectral library
A mass spectral library consisting of tryptic peptide product ion spectra generated by liquid chromatography coupled to ion trap mass spectrometry (LC-ITMS). Developed using samples derived from Arabidopsis thaliana and Medicago truncatula. The database serves as a reference and can be used for protein identification in uncharacterized samples. Protein identification by ProMEX is linked to other molecular levels of biological organization such as metabolite, pathway and transcript data.
Available data
Example queries
website/prophecy.html 0000644 0002441 0001757 00000003027 11606605755 015046 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PROPHECY profiling of phenotypic characteristics in yeast
Quantitative information about phenotypes for the complete collection of deletion strains in yeast (Saccharomyces cerevisiae).
website/prorule.html 0000644 0002441 0001757 00000003742 11606605755 014711 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ProRule collection of rules based on PROSITE predictors
ProRule section of PROSITE is constituted of manually created rules that increase the discriminatory power of PROSITE motifs (generally profiles) by providing additional information about functionally and/or structurally critical amino acids and can automatically generate annotation based on PROSITE motifs in the UniProtKB/Swiss-Prot format. Each ProRule is defined in the UniRule format.
website/prosas.html 0000644 0002441 0001757 00000003236 11606605755 014526 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Protein Structure and Alternative Splicing database (ProSAS)
Unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. Annotates protein structures for several Ensembl genomes. Alternative transcripts can be analyzed on the protein structure and protein function level.
website/prosat2.html 0000644 0002441 0001757 00000002510 11606605755 014603 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PROSAT2 protein structure annotation tool
Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein.
website/prosite.html 0000644 0002441 0001757 00000011136 11606605755 014702 0 ustar jison industry
Bioinformatics Data Resource Catalogue
A Database of protein domains, families and functional sites
Documentation for protein domains, families and functional sites as well as associated patterns and profiles to identify them.
Available data
Example queries
website/protclustdb.html 0000644 0002441 0001757 00000006150 11606605755 015562 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Entrez Protein Clusters
Entrez Protein Clusters
Available data
Example queries
website/proteinmodelportal.html 0000644 0002441 0001757 00000005530 11606605755 017141 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase
Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase
Available data
Example queries
website/protepedia.html 0000644 0002441 0001757 00000002523 11606605755 015351 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Protepedia collaborative 3D protein encyclopedia
Free, collaborative 3D encyclopedia of proteins & other molecules.
website/proteus.html 0000644 0002441 0001757 00000003061 11606605755 014714 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Protein terminus short linear sequences
Tool for identification of short linear signatures in protein termini, based on a positional-based search method for revealing short significant signatures in termini of proteins.
website/protonet.html 0000644 0002441 0001757 00000007551 11606605755 015075 0 ustar jison industry
Bioinformatics Data Resource Catalogue
ProtoNet automatic hierarchical classification of proteins
Automatic hierarchical classification of protein sequences.
Available data
Example queries
website/pseudobase.html 0000644 0002441 0001757 00000002443 11606605756 015351 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PseudoBase RNA pseudoknots database
Collection of RNA pseudoknots.
website/pseudocap.html 0000644 0002441 0001757 00000007753 11606605756 015213 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PseudoCAP pseudomonas genome database
Pseudomonas genome database.
Available data
Example queries
website/pstiing.html 0000644 0002441 0001757 00000004077 11606605756 014701 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Protein, signalling, transcriptional interactions and inflammation networks gateway (pSTIING)
Protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast.
website/ptch.html 0000644 0002441 0001757 00000003403 11606605756 014152 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PTCH mutation database
Information on mutations and polymorphisms in the PTCH1 gene. The human homologue of Drosophila patched, PTCH1, has been identified as the gene underlying the cancer predisposition syndrome Nevoid Basal Cell Carcinoma Syndrome (NBCCS, OMIM 109400). This syndrome is also known as Gorlin's syndrome or Basal Cell Nevus Syndrome.
website/pubchem.html 0000644 0002441 0001757 00000002454 11606605756 014644 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PubChem
Information on the biological activities of small molecules, including bioassay records, chemical structures and substances.
website/pubmeth.html 0000644 0002441 0001757 00000010170 11606605756 014657 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PubMeth reviewed methylation database in cancer
An annotated and reviewed database of methylation in cancer. It is based on automated textmining of literature and is afterwards manually curated and annotated.
Available data
Example queries
website/rat-heart-2dpage.html 0000644 0002441 0001757 00000005724 11606605756 016253 0 ustar jison industry
Bioinformatics Data Resource Catalogue
2-DE database of rat heart, at German Heart Institute Berlin, Germany
2-DE database of rat heart, at German Heart Institute Berlin, Germany
Available data
Example queries
website/ratmap.html 0000644 0002441 0001757 00000003172 11606605756 014503 0 ustar jison industry
Bioinformatics Data Resource Catalogue
RATMAP rat genome database
Rat genome database.
Example queries
| Data |
Format |
Query |
Example |
website/rb1genemutation.html 0000644 0002441 0001757 00000002407 11606605756 016323 0 ustar jison industry
Bioinformatics Data Resource Catalogue
RB1 gene mutation database (RB1GeneMutation)
Retinoblastoma genetics database.
website/rdg.html 0000644 0002441 0001757 00000002606 11606605756 013774 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Rat genome database (RDG)
Rat genome database.
website/reactome.html 0000644 0002441 0001757 00000027003 11606605756 015015 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Reactome knowledgebase of biological pathways
Curated knowledgebase of biological pathways and processes.
Available data
Example queries
website/rebase.html 0000644 0002441 0001757 00000007230 11606605756 014457 0 ustar jison industry
Bioinformatics Data Resource Catalogue
REBASE restriction enzymes and methylases database
Restriction enzymes and methylases database.
Available data
Example queries
website/redidb.html 0000644 0002441 0001757 00000013707 11606605756 014455 0 ustar jison industry
Bioinformatics Data Resource Catalogue
RNA editing database (REDIdb)
Sequences post-transcriptionally modified by RNA editing from primary databases and literature. All editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored.
Available data
Example queries
website/refseq.html 0000644 0002441 0001757 00000006423 11606605756 014506 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NCBI reference sequences
A comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. Provides a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.
Available data
Example queries
website/repairtoire.html 0000644 0002441 0001757 00000002733 11606605756 015546 0 ustar jison industry
Bioinformatics Data Resource Catalogue
REPAIRtoire DNA repair pathways
Components involved in the repair mechanisms for all kinds of cellular DNA lesions. Four repair pathways (from H.sapiens, E.coli and S.cerevisiae) are contained, together with their protein components and molecular events that trigger those pathways.
website/reproduction-2dpage.html 0000644 0002441 0001757 00000007623 11606605756 017101 0 ustar jison industry
Bioinformatics Data Resource Catalogue
REPRODUCTION-2DPAGE database
REPRODUCTION-2DPAGE 2D gel protein database.
Available data
Example queries
website/resid.html 0000644 0002441 0001757 00000005464 11606605756 014333 0 ustar jison industry
Bioinformatics Data Resource Catalogue
RESID database of protein modifications
A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
Available data
Example queries
website/retroryza.html 0000644 0002441 0001757 00000002674 11606605756 015266 0 ustar jison industry
Bioinformatics Data Resource Catalogue
RetrOryza database of rice LTR retrotransposons
Information and resources related to LTR-retrotransposons in rice genome.
website/rfam.html 0000644 0002441 0001757 00000013535 11606605756 014150 0 ustar jison industry
Bioinformatics Data Resource Catalogue
RNA families database of alignments and CMs
Collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. The main use of Rfam is as a source of RNA multiple alignments with consensus secondary structure annotation in a consistent format.
Available data
Example queries
website/rgd.html 0000644 0002441 0001757 00000010541 11606605756 013771 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Rat genome database
Rat genome database (RGD) goal is to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data.
Available data
Example queries
website/rhea.html 0000644 0002441 0001757 00000002763 11606605757 014144 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Rhea
A reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions.
website/rissc.html 0000644 0002441 0001757 00000002467 11606605757 014351 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ribosomal internal spacer sequence collection (RISSC)
Ribosomal 16S-23S spacer sequences intended mainly for molecular biology studies in typing, phylogeny and population genetics.
website/rna-frabase.html 0000644 0002441 0001757 00000002604 11606605757 015400 0 ustar jison industry
Bioinformatics Data Resource Catalogue
RNA FRABASE database
Database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation.
website/rnavirusdb.html 0000644 0002441 0001757 00000005403 11606605757 015376 0 ustar jison industry
Bioinformatics Data Resource Catalogue
RNA virus genome database (RNAVirusDB)
RNA virus genome database.
Available data
Example queries
website/rnrdb.html 0000644 0002441 0001757 00000003267 11606605757 014334 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Ribonucleotide reductase database (RNRdb)
Compilation of all published 3D structures of different RNR proteins as well as a compilation of all mutant proteins constructed including links to the relevant publication(s). It is used to retrieve RNR protein sequences from any organism that have been either experimentally characterised or predicted from genome sequence data.
website/rouge.html 0000644 0002441 0001757 00000006321 11606605757 014340 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Rodent unidentified gene-encoded large proteins database (Rouge)
A sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs).
Available data
Example queries
website/rsitedb.html 0000644 0002441 0001757 00000003413 11606605757 014652 0 ustar jison industry
Bioinformatics Data Resource Catalogue
RNA binding site database (RsiteDB)
Interactions of extruded, unpaired RNA nucleotide bases. It presents and classifies the protein binding pockets that accommodate them. It allows the recognition of similar protein binding patterns involved in interactions with different RNA molecules. Given an unbound structure of a target protein it allows the prediction of its RNA nucleotide binding sites.
website/rtkdb.html 0000644 0002441 0001757 00000002372 11606605757 014327 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Receptor tyrosine kinase database (RTKdb)
Receptor tyrosine kinase database.
website/rtprimerdb.html 0000644 0002441 0001757 00000003065 11606605757 015373 0 ustar jison industry
Bioinformatics Data Resource Catalogue
PCR primers and probes database (RTPrimerDB)
Database of primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different laboratories.
website/s4.html 0000644 0002441 0001757 00000002564 11606605757 013552 0 ustar jison industry
Bioinformatics Data Resource Catalogue
S4 structure-based sequence alignments of SCOP superfamilies
An automatically generated database of multiple structure-based sequence alignments of protein superfamilies in the SCOP database.
website/sabio-rk.html 0000644 0002441 0001757 00000011225 11606605757 014725 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database for biochemical reactions and their kinetics.
Biochemical pathways and reaction kinetics.
Available data
Example queries
website/saffron_genes.html 0000644 0002441 0001757 00000002654 11606605757 016043 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Saffron genes database
EST sequences from saffron (Crocus sativus) stigmas.
website/scop.html 0000644 0002441 0001757 00000011633 11606605757 014165 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Structural classification of proteins (SCOP) database
The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
Available data
Example queries
website/scoppi.html 0000644 0002441 0001757 00000002713 11606605757 014515 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Structural Classification of Protein-Protein Interfaces (SCOPPI)
Domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions. Interfaces are classified according to the geometry of the domain associations and are annotated with various interaction characteristics.
website/scowl.html 0000644 0002441 0001757 00000006401 11606605757 014345 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Structural characterization of water, ligands and proteins (SCOWL)
PDB interface interactions at atom, residue and domain level. The database contains protein interfaces and residue-residue interactions formed by structural units and interacting solvent.
Available data
Example queries
website/seattlesnps.html 0000644 0002441 0001757 00000006253 11606605757 015570 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SeattleSNPs variation discovery resource
Database for identifying, genotyping, and modelling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans.
Available data
Example queries
website/sebida.html 0000644 0002441 0001757 00000003206 11606605757 014445 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Sebida sex-biased genes
Functional and evolutionary analysis of sex-biased genes. Sebida integrates data from multiple microarray studies comparing male versus female gene expression in D. melanogaster, D. simulans, and A. gambiae.
website/seed.html 0000644 0002441 0001757 00000011105 11606605757 014133 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The SEED genome comparison environment
Environment for comparative genome analysis.
Available data
Example queries
website/selectome.html 0000644 0002441 0001757 00000022774 11606605757 015211 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Selectome database of positive selection
Database of positive selection based on a rigorous branch-site specific likelihood test.
Available data
Example queries
website/sgd.html 0000644 0002441 0001757 00000012312 11606605757 013771 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Saccharomyces genome database (SGD)
Database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
Available data
Example queries
website/siena-2dpage.html 0000644 0002441 0001757 00000005663 11606605757 015466 0 ustar jison industry
Bioinformatics Data Resource Catalogue
2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy
2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy
Available data
Example queries
website/signalinggateway.html 0000644 0002441 0001757 00000002756 11606605760 016556 0 ustar jison industry
Bioinformatics Data Resource Catalogue
UCSD-Nature Signaling Gateway Molecule Pages
Information on over 4000 proteins involved in cellular signaling. Each 'molecule page' contains regularly updated information derived from public data sources as well as sequence analysis, references and links to other databases.
website/silva-lsu.html 0000644 0002441 0001757 00000006024 11606605760 015130 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SILVA ribosomal RNA sequence data (large subunit)
SILVA provides comprehensive, quality checked and regularly updated databases of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).
Available data
Example queries
website/silva-ssu.html 0000644 0002441 0001757 00000006004 11606605760 015135 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SILVA ribosomal RNA sequence data (small subunit)
SILVA provides comprehensive, quality checked and regularly updated databases of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).
Available data
Example queries
website/simap.html 0000644 0002441 0001757 00000013421 11606605760 014321 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Similarity matrix of proteins (SIMAP)
Pre-calculated protein similarities. It contains published protein sequences and is continuously updated.
Available data
Example queries
website/sirnadb.html 0000644 0002441 0001757 00000002332 11606605760 014631 0 ustar jison industry
Bioinformatics Data Resource Catalogue
siRNAdb database
siRNAdb database
website/sisyphus.html 0000644 0002441 0001757 00000005427 11606605760 015106 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SISYPHUS database of protein structure alignments
Structural alignments for proteins with non-trivial relationships.
Available data
Example queries
website/sitesbase.html 0000644 0002441 0001757 00000003660 11606605760 015176 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SitesBase database
Known ligand binding sites within PDB navigable by PDB identifier or ligand 3 letter code e.g. NAD. Each binding site has a frequently updated register of structurally similar binding sites sharing atomic similarity detected by geometric hashing. Multiple alignments, structural superpositions and links to other structural databases are also available enabling further analysis.
website/s_martdb.html 0000644 0002441 0001757 00000002737 11606605757 015021 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The S/MAR transaction database (S/MARtDB)
Information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. It covers the whole range from yeast to human.
website/smart.html 0000644 0002441 0001757 00000010011 11606605760 014326 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Simple modular architecture research tool (SMART)
SMART protein domain database.
Available data
Example queries
website/smpdb.html 0000644 0002441 0001757 00000003405 11606605760 014316 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Small Molecule Pathway Database (SMPDB)
Small molecule pathways found in humans. It provides detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures.
website/smr.html 0000644 0002441 0001757 00000005666 11606605760 014025 0 ustar jison industry
Bioinformatics Data Resource Catalogue
A database of annotated 3D protein structure models
Annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.
Available data
Example queries
website/snap.html 0000644 0002441 0001757 00000002354 11606605760 014154 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SNAP database of human gene variations
Human gene variations.
website/snappi.html 0000644 0002441 0001757 00000003360 11606605760 014503 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SNAPPI database of structures, interfaces and alignments for protein-protein interactions
Structures, interfaces and alignments for protein-protein interactions.
website/snornabase.html 0000644 0002441 0001757 00000002475 11606605760 015352 0 ustar jison industry
Bioinformatics Data Resource Catalogue
snoRNABase database of human H/ACA and C/D box snoRNAs
Human H/ACA and C/D box snoRNAs.
website/sno_scarnabase.html 0000644 0002441 0001757 00000002615 11606605760 016174 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Small nucleolar RNA and small cajal body-specific RNA database (sno/scaRNAbase)
sno/scaRNA-associated genetic and functional data, from several database sources via web-accessible search interfaces.
website/snpeffect.html 0000644 0002441 0001757 00000003200 11606605760 015157 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SNPeffect database of molecular phenotyping of human SNPs and disease mutations
Molecular phenotyping of human SNPs and disease mutations.
website/snpnexus.html 0000644 0002441 0001757 00000002343 11606605760 015074 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SNPnexus database for SNP selection
SNP selection database.
website/snpstr.html 0000644 0002441 0001757 00000003407 11606605760 014544 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SNPSTR databasee
Database of compound genetic marker called SNPSTR which combines a STR marker with one or more tightly linked SNPs. Here, the SNP(s) and the microsatellite are less than 250 base pairs apart so each SNPSTR can be considered a small haplotype with no recombination occurring between the two individual markers.
website/source.html 0000644 0002441 0001757 00000010662 11606605760 014514 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The Stanford online universal resource for Clones and ESTs (SOURCE)
A unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports.
Available data
Example queries
website/soybase.html 0000644 0002441 0001757 00000002734 11606605760 014662 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SoyBase soybean genome database
Database of soybean genetics and molecular biology.
website/spliceaid.html 0000644 0002441 0001757 00000006570 11606605760 015154 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SpliceAid database of strictly experimentally assessed target RNA sequences in humans
Experimental RNA target motifs bound by splicing proteins in humans.
Available data
Example queries
website/splicenest.html 0000644 0002441 0001757 00000002740 11606605760 015363 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SpliceNest database
Visualizing splicing of genes from EST Data, based on mappings of the GeneNest EST Contigs to genomic sequence.
website/spodobase.html 0000644 0002441 0001757 00000003207 11606605761 015171 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Spodoptera frugiperda database (SpodoBase)
An integrated database for the genomics of the Lepidoptera Spodoptera frugiperda.
website/stcdb.html 0000644 0002441 0001757 00000002454 11606605761 014314 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Signal transduction classification database (STCDB)
Signal transduction classification.
website/stitch.html 0000644 0002441 0001757 00000002600 11606605761 014504 0 ustar jison industry
Bioinformatics Data Resource Catalogue
STITCH chemical-protein interactions
A resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.
website/straininfo.net.html 0000644 0002441 0001757 00000002441 11606605761 016152 0 ustar jison industry
Bioinformatics Data Resource Catalogue
StrainInfo.net bioportal
Search the holdings of multiple biological resource centres (BRCs) through a single web interface.
website/strepto-db.html 0000644 0002441 0001757 00000002535 11606605761 015300 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Strepto-DB comparative genomics of group A and group B streptococci
Database for comparative genome analyses of group A and group B streptococci.
website/string.html 0000644 0002441 0001757 00000007765 11606605761 014535 0 ustar jison industry
Bioinformatics Data Resource Catalogue
STRING protein-protein interaction database
Known and predicted protein-protein interactions.
Available data
Example queries
website/structurallyconservedinterfaces.html 0000644 0002441 0001757 00000003061 11606605761 021742 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Structurally conserved interfaces
Structures of protein-protein interfaces from PDB.
website/sulfolobus.html 0000644 0002441 0001757 00000002575 11606605761 015416 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Sulfolobus genome database
The three sequenced Sulfolobus genomes.
website/superdrug.html 0000644 0002441 0001757 00000002265 11606605761 015235 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SuperDrug drug database
Drug compounds with conformers.
website/superhapten.html 0000644 0002441 0001757 00000003045 11606605761 015550 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SuperHapten immunogenic compound database
Database of haptens, related antibodies and carriers.
website/supernatural.html 0000644 0002441 0001757 00000002335 11606605761 015740 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SuperNatural natural compound database
A searchable database of natural compounds.
website/superscent.html 0000644 0002441 0001757 00000002262 11606605761 015405 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Superscent database of scents
Database of scent molecules.
website/supersite.html 0000644 0002441 0001757 00000003722 11606605761 015237 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SuperSite dictionary of metabolite and drug binding sites in proteins
A ligand and binding site oriented view of the protein structural space. SuperSite integrates evolutionary information in the proteins as well as predicted binding sites from LigsiteCSC.
website/supertarget-matador.html 0000644 0002441 0001757 00000003150 11606605761 017201 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SuperTarget and Matador database
Enzyme, drug and pathways database.
website/supertoxic.html 0000644 0002441 0001757 00000002317 11606605761 015420 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Supertoxic toxic compounds database
Database of toxic compounds with synonyms.
website/supfam.html 0000644 0002441 0001757 00000003361 11606605761 014506 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Superfamily database of structural and functional annotation
Structural and functional protein annotations (via HMM library) for all completely sequenced organisms.
website/surface.html 0000644 0002441 0001757 00000002725 11606605761 014646 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SURFACE database of protein surface patches
Surface residues and functions, annotated, compared and evaluated.
website/swiss-2dpage.html 0000644 0002441 0001757 00000020647 11606605762 015532 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Two-dimensional polyacrylamide gel electrophoresis database (SWISS-2DPAGE)
Data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps.
Available data
Example queries
website/swissregulon.html 0000644 0002441 0001757 00000004522 11606605762 015760 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SwissRegulon database of regulatory site annotations
Genome-wide annotations of regulatory sites.
Available data
website/systers.html 0000644 0002441 0001757 00000002645 11606605762 014734 0 ustar jison industry
Bioinformatics Data Resource Catalogue
SYSTERS protein family database
Large-scale protein clustering based on sequence similarity.
website/systomonas.html 0000644 0002441 0001757 00000002471 11606605762 015434 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Systomonas database for systems biology of Pseudomonads
Molecular networks in pseudomonads with focus on Pseudomonas aeruginosa.
website/sysznfc2h2.html 0000644 0002441 0001757 00000002600 11606605762 015222 0 ustar jison industry
Bioinformatics Data Resource Catalogue
C2H2 zinc finger gene database (SysZNFC2H2)
An information resource for C2H2 Zinc Finger genes in human and mouse.
website/t1dbase.html 0000644 0002441 0001757 00000002515 11606605762 014537 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Type 1 diabetes database (T1Dbase)
Database for type 1 diabetes (T1D): the genetics of T1D susceptibility and beta cell biology.
website/t3db.html 0000644 0002441 0001757 00000003100 11606605763 014040 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Toxin and Toxin Target Database (T3DB)
Toxin data with comprehensive toxin target information. Toxins are described by synonyms and include pollutants, pesticides, drugs, and food toxins, which are linked to corresponding toxin target records. Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information.
website/taed.html 0000644 0002441 0001757 00000002356 11606605762 014134 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The adaptive evolution database (TAED)
Protein-encoding gene families.
website/tair.html 0000644 0002441 0001757 00000012123 11606605762 014147 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The Arabidopsis information resource (TAIR)
Comprehensive information resources for Arabidopsis.
Available data
Example queries
website/tarbase.html 0000644 0002441 0001757 00000002335 11606605762 014635 0 ustar jison industry
Bioinformatics Data Resource Catalogue
miRNA target database (TarBase)
The database of experimentally supported targets.
website/tassdb.html 0000644 0002441 0001757 00000006165 11606605762 014501 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Tandem splice site database
TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors.
Available data
Example queries
website/taxon.html 0000644 0002441 0001757 00000005201 11606605762 014340 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NCBI's taxonomic identifier
NCBI's taxonomic identifier
Available data
Example queries
website/tbmap.html 0000644 0002441 0001757 00000003050 11606605762 014312 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Mapping names in TreeBASE
TBMap is a project to map names in the the phylogenetic database TreeBASE to names in taxonomic databases, such as uBio, ITIS, IPNI, and the NCBI taxonomy database.
website/tcacycle.html 0000644 0002441 0001757 00000005557 11606605762 015014 0 ustar jison industry
Bioinformatics Data Resource Catalogue
TCA cycle gene mutation database
TCA cycle gene mutation database.
Available data
Example queries
website/tcdb.html 0000644 0002441 0001757 00000006216 11606605762 014132 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Transport classification database
A comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally.
Available data
Example queries
website/tdr.html 0000644 0002441 0001757 00000002614 11606605762 014005 0 ustar jison industry
Bioinformatics Data Resource Catalogue
TDR targets database
Identification and ranking of targets against neglected tropical diseases.
website/tigrfams.html 0000644 0002441 0001757 00000005750 11606605762 015034 0 ustar jison industry
Bioinformatics Data Resource Catalogue
A protein family database
Protein families based on hidden Markov models (HMMs).
Available data
Example queries
website/tigr.html 0000644 0002441 0001757 00000005574 11606605762 014171 0 ustar jison industry
Bioinformatics Data Resource Catalogue
TIGR
The bacterial database(s) of The Institute of Genome Research
The TIGR bacterial Genome Annotation Database.
Available data
Example queries
website/tmadb.html 0000644 0002441 0001757 00000002753 11606605763 014310 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Tissue microarray database
Tissue microarray (TMA) database for archiving all aspects of data associated with TMAs.
website/tomatestdb.html 0000644 0002441 0001757 00000002476 11606605763 015371 0 ustar jison industry
Bioinformatics Data Resource Catalogue
An EST database from multiple Tomato species
A collection of tomato EST sequences downloaded from dbEST.
website/topdb.html 0000644 0002441 0001757 00000013261 11606605763 014325 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Topology of transmembrane proteins
Transmembrane protein datasets containing experimentally derived topology information.
Available data
Example queries
website/topdom.html 0000644 0002441 0001757 00000003420 11606605763 014513 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Transmembrane domains and motifs
A collection of domains and sequence motifs located conservatively in one side of transmembrane proteins.
website/transdab.html 0000644 0002441 0001757 00000005171 11606605763 015014 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Database of transglutaminase substrate proteins
Database of transglutaminase substrate proteins.
Available data
Example queries
website/transpath.html 0000644 0002441 0001757 00000003726 11606605763 015226 0 ustar jison industry
Bioinformatics Data Resource Catalogue
TRANSPATH database
Information on signaling molecules, metabolic enzymes, second messengers, endogenous metabolites, miRNAs and the reactions they are involved in, resulting in a complex network of interconnected chains of reactions and pathways.
website/transpogene.html 0000644 0002441 0001757 00000002464 11606605763 015545 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Transposed elements in proteins for 7 organisms
Data on the influence of Transposed Elements (TEs) on the transcriptome of 7 species.
website/trbase.html 0000644 0002441 0001757 00000002322 11606605763 014471 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Tandem repeats database
Tandem repeats in the human genome.
website/treefam.html 0000644 0002441 0001757 00000003045 11606605763 014637 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Phylogenetic trees of animal genes
Phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families.
website/trnasequences.html 0000644 0002441 0001757 00000003237 11606605763 016077 0 ustar jison industry
Bioinformatics Data Resource Catalogue
tRNA sequences database
Compilation of tRNA sequences and sequence of tRNA genes.
website/tropgene-db.html 0000644 0002441 0001757 00000002377 11606605763 015431 0 ustar jison industry
Bioinformatics Data Resource Catalogue
TropGENE database
Genetic and genomic information about tropical crops studied by Cirad.
website/trsdb.html 0000644 0002441 0001757 00000003224 11606605763 014331 0 ustar jison industry
Bioinformatics Data Resource Catalogue
TrSDB transcription factors
Biological Proteome KnowledgeBase linking IPI and SPTR-NR based Proteome analyses with TranScout, TransMem and ProtLoc and offering crosslinks with other relevant biodatabases such as SWISS-PROT, NCBI Refseq, Ensembl, InterPro or Gene Ontology Annotation.
website/ttd.html 0000644 0002441 0001757 00000003355 11606605762 014012 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Therapeutic Target Database (TTD)
A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information provided are fully referenced.
website/tuberculist.html 0000644 0002441 0001757 00000006320 11606605763 015560 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Mycobacterium tuberculosis strain H37Rv genome database
Mycobacterium tuberculosis strain H37Rv genome database
Available data
Example queries
website/u12db.html 0000644 0002441 0001757 00000002373 11606605763 014134 0 ustar jison industry
Bioinformatics Data Resource Catalogue
U12-type intron database
U12-type intron database
website/ucd-2dpage.html 0000644 0002441 0001757 00000004272 11606605763 015132 0 ustar jison industry
Bioinformatics Data Resource Catalogue
University College Dublin 2-DE Proteome Database
University College Dublin 2-DE Proteome Database
Available data
website/ucsc.html 0000644 0002441 0001757 00000005312 11606605763 014150 0 ustar jison industry
Bioinformatics Data Resource Catalogue
UCSC genome browser
UCSC genome browser
Available data
Example queries
website/umd-dmd.html 0000644 0002441 0001757 00000002657 11606605763 014553 0 ustar jison industry
Bioinformatics Data Resource Catalogue
UMD-DMD France genotype-phenotype dystrophinopathy patients
Knowledgebase related to mutations of the DMD gene.
website/umd.html 0000644 0002441 0001757 00000002325 11606605764 014002 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Universal mutation database
Collection of mutations in human genes associated with genetic diseases.
website/unigene.html 0000644 0002441 0001757 00000006312 11606605763 014646 0 ustar jison industry
Bioinformatics Data Resource Catalogue
UniGene gene-oriented nucleotide sequence clusters
Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
Available data
Example queries
| Data |
Format |
Query |
Example |
website/unihi.html 0000644 0002441 0001757 00000002367 11606605763 014336 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Unified human interactome database
Protein interaction analysis.
website/unilib.html 0000644 0002441 0001757 00000002600 11606605763 014472 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Unified library database
A library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap.
website/uniparc.html 0000644 0002441 0001757 00000005646 11606605764 014667 0 ustar jison industry
Bioinformatics Data Resource Catalogue
UniProt Archive
Part of UniProt project - a non-redundant archive of protein sequences extracted from public databases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, PIR-PSD, EMBL, EMBL WGS, Ensembl, IPI, PDB, PIR-PSD, RefSeq, FlyBase, WormBase, H-Invitational Database, TROME database, European Patent Office proteins, United States Patent and Trademark Office proteins (USPTO) and Japan Patent Office proteins.
Available data
Example queries
website/unipathway.html 0000644 0002441 0001757 00000002676 11606605764 015417 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Unipathway
A manually curated database of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled vocabulary to describe the role of a protein in a metabolic pathway.
website/uniprot.html 0000644 0002441 0001757 00000014573 11606605764 014725 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Universal protein resource
A comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
Available data
Example queries
website/uniprotkb_swiss-prot.html 0000644 0002441 0001757 00000014753 11606605764 017454 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Universal protein resource knowledge base / Swiss-Prot
Section of the UniProt knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature
Available data
Example queries
website/uniprotkb_trembl.html 0000644 0002441 0001757 00000014646 11606605764 016610 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Universal protein resource knowledge base / Swiss-Prot
Section of the UniProt knowledgebase, containing computationally analysed records waiting for full manual annotation
Available data
Example queries
website/uniref.html 0000644 0002441 0001757 00000033267 11606605764 014516 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Non-redundant reference (UniRef) databases
Clustered sets of sequences from UniProt Knowledgebase (including splice variants and isoforms) and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.
Available data
Example queries
website/unisave.html 0000644 0002441 0001757 00000002432 11606605764 014666 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Uniprot version archive
A repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions.
website/unists.html 0000644 0002441 0001757 00000005542 11606605764 014546 0 ustar jison industry
Bioinformatics Data Resource Catalogue
NCBI database of sequence tagged sites
A comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.
Available data
Example queries
website/unite.html 0000644 0002441 0001757 00000005220 11606605764 014336 0 ustar jison industry
Bioinformatics Data Resource Catalogue
UNITE rDNA sequences from ectomycorrhizal asco- and basidiomycetes
UNITE is a rDNA sequence database focused on ectomycorrhizal asco- and basidiomycetes.
Available data
Example queries
website/unitrap.html 0000644 0002441 0001757 00000005363 11606605764 014704 0 ustar jison industry
Bioinformatics Data Resource Catalogue
UniTrap gene trap clones
Tools for the biologist enabling optimized use of gene trap clones.
Available data
Example queries
website/utilldb.html 0000644 0002441 0001757 00000002611 11606605764 014652 0 ustar jison industry
Bioinformatics Data Resource Catalogue
URGV TILLING platform databases
Lines, phenotype categories, sequences and mutations for pea and tomatoe.
website/utrdb.html 0000644 0002441 0001757 00000022420 11606605764 014333 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Regulatory motifs in eukaryotic UTRs
UTResource collect data and analysis tool for the functional classification of 5' and 3'UTRs of eukaryotic mRNAs.
Available data
Example queries
website/utrsite.html 0000644 0002441 0001757 00000006060 11606605764 014714 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Regulatory motifs in eukaryotic UTRs
UTRSite is a collection of functional sequence patterns located in 5' or 3' UTR sequences.
Available data
Example queries
website/vbase2.html 0000644 0002441 0001757 00000005536 11606605764 014406 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse
An integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.
Available data
Example queries
website/vectorbase.html 0000644 0002441 0001757 00000011750 11606605764 015354 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Invertebrate vectors of human pathogens
Invertebrate vectors of human pathogens.
Available data
Example queries
website/vega.html 0000644 0002441 0001757 00000002456 11606605764 014144 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Vertebrate Genome Annotation (VEGA) database
A central repository for high quality, frequently updated, manual annotation of vertebrate finished genome sequence.
website/vida.html 0000644 0002441 0001757 00000003626 11606605764 014145 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Virus Database at University College London
VIDA contains a collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family, you can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures.
website/virusmint.html 0000644 0002441 0001757 00000003114 11606605764 015252 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Viral protein interaction
VirusMINT aims at collecting and annotating in a structured format all the interactions between human and viral proteins and to integrate this information in the human protein interaction network.
website/vsgdb.html 0000644 0002441 0001757 00000002576 11606605764 014332 0 ustar jison industry
Bioinformatics Data Resource Catalogue
A database of trypanosomal variant surface glycoproteins
A database of trypanosomal variant surface glycoproteins.
website/worfdb.html 0000644 0002441 0001757 00000005370 11606605764 014503 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The C.elegans ORFeome cloning project
The Caenorhabditis elegans ORFeome cloning project
Available data
Example queries
website/world-2dpage_0003.html 0000644 0002441 0001757 00000006054 11606605761 016146 0 ustar jison industry
Bioinformatics Data Resource Catalogue
World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome
World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome.
Available data
Example queries
website/world-2dpage_0004.html 0000644 0002441 0001757 00000005562 11606605761 016152 0 ustar jison industry
Bioinformatics Data Resource Catalogue
World-wide gel-based proteomics database (0004) for mature rat olfactory bulb
World-wide gel-based proteomics database (0004) for mature rat olfactory bulb.
Available data
Example queries
website/world-2dpage_0005.html 0000644 0002441 0001757 00000005674 11606605762 016160 0 ustar jison industry
Bioinformatics Data Resource Catalogue
World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose
World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose.
Available data
Example queries
website/world-2dpage_0006.html 0000644 0002441 0001757 00000005623 11606605762 016153 0 ustar jison industry
Bioinformatics Data Resource Catalogue
World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee
World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee.
Available data
Example queries
website/world-2dpage_cgl14067-2dpage.html 0000644 0002441 0001757 00000005573 11606605761 020100 0 ustar jison industry
Bioinformatics Data Resource Catalogue
World-wide gel-based proteomics database (CGL14067-2DPAGE)
World-wide gel-based proteomics database (CGL14067-2DPAGE)
Available data
Example queries
website/world-2dpage.html 0000644 0002441 0001757 00000005663 11606605765 015515 0 ustar jison industry
Bioinformatics Data Resource Catalogue
The world-2DPAGE database
A public repository, standards compliant, for proteomics image data published in the literature.
Available data
Example queries
website/world-2dpage_nibr_2d-page.html 0000644 0002441 0001757 00000005546 11606605761 020022 0 ustar jison industry
Bioinformatics Data Resource Catalogue
World-wide gel-based proteomics database (NIBR 2D-PAGE)
World-wide gel-based proteomics database (NIBR 2D-PAGE)
Available data
Example queries
website/wormbase.html 0000644 0002441 0001757 00000011571 11606605765 015040 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Caenorhabditis elegans genome database
Caenorhabditis elegans genome database
Available data
Example queries
website/xenbase.html 0000644 0002441 0001757 00000006470 11606605765 014650 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Xenopus laevis and tropicalis biology and genomics resource
Xenopus laevis and tropicalis biology and genomics resource
Available data
Example queries
website/yeast_complexes.html 0000644 0002441 0001757 00000002732 11606605765 016424 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Yeast complexes database
Information on protein-protein interactions and protein complexes in yeast.
website/yeast-gfp.html 0000644 0002441 0001757 00000004456 11606605765 015124 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Yeast GFP fusion localization database
Yeast GFP fusion localization database
Available data
website/yeastract.html 0000644 0002441 0001757 00000024512 11606605765 015217 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Transcriptional regulators database
A curated repository of more than 34469 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1000 bibliographic references. It also includes the description of 291 specific DNA binding sites for more than a hundred characterized TFs.
Available data
Example queries
website/ygob.html 0000644 0002441 0001757 00000005510 11606605765 014155 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Yeast gene order browser
Tool for visualising the syntenic context of any gene from several yeast genomes.
Available data
Example queries
website/ymgv.html 0000644 0002441 0001757 00000003472 11606605765 014204 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Yeast microarray global viewer
Transcriptional expression profiles of yeast genes among most of the published expression datasets.
website/zfin.html 0000644 0002441 0001757 00000006144 11606605765 014167 0 ustar jison industry
Bioinformatics Data Resource Catalogue
Zebrafish information network genome database
Zebrafish information network genome database
Available data
Example queries