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Database Archive

Databases

Protein related databases

UniProt - the universal protein resource (including UniProtKB -Swiss-Prot and TrEMBL-, UniRef, UniParc)
Around UniProtKB - links to related databases and portals
- HAMAP - Portal to microbial UniProtKB/Swiss-Prot entries
- SwissVar - Portal to human diseases and variant information in UniProtKB/Swiss-Prot
- UniPathway - Metabolic pathways database
- ViralZone - Portal to viral UniProtKB/Swiss-Prot entries
- HPI - Human Proteomics Initiative
- PPAP - Plant Proteome Annotation Project
- Tox-Prot - Toxin Annotation Project
Swiss Human Plasma protein dataset - Novartis/Geneprot MicroProt2 dataset from Human Plasma samples
NCBI protein resources
InterPro - Integrated Resources of Proteins Domains and Functional Sites
PROSITE - Database of protein families and domains
BLOCKS - BLOCKS db
Gene3D - Structural and Functional Annotation of Protein Families
Panther - Functional classification system
Pfam - Protein families db (HMM derived) [Mirrors at JFRC (USA), CCBB (South Korea) Institute, UK, Karolinska Institutet (Sweden)]
PIRSF - Protein classification system
PRINTS - Protein Motif fingerprint db
ProDom - Protein domain db (Automatically generated)
SBASE - SBASE domain db
SMART - Simple Modular Architecture Research Tool
SUPERFAMILY - Library of profile HMMs representing all proteins of known structure
STRING - Search Tool for the Retrieval of Interacting Genes/Proteins
TIGRFAMs - TIGR protein families db
BIND - Biomolecular Interaction Network Database
DIP - Database of Interacting Proteins
MINT - Molecular INTeraction database
HPRD - Human Protein Reference Database
IntAct
BioGRID - General Repository for Interaction Dataset
PPI - JCB Protein-Protein Interaction Website
PMD - Protein Mutant db

Protein 3D structure related databases

PDB - Protein Data Bank
PDBTM - Protein Data Bank of Transmembrane Proteins
BioMagResBank - Repository for data on proteins, peptides, and nucleic acids from NMR spectroscopy
SWISS-MODEL Repository - Automatically generated protein models db
ModBase - Db of comparative protein structure models
CATH - UCL BSM structural classification of proteins
SCOP - Structural classification of proteins [ Mirrors]
HCA - Hydrophobic Cluster Database
Molecules To Go - Molecules To Go (formerly known as Molecules R Us), browser for PDB
BMM Domain Fishing - Biomolecular Modelling Laboratory (ICRF) protein domain fishing
Relibase - Receptor/ligand complexes db [Mirror in USA]
CCDC - Cambridge Crystallographic Data Center (Cambridge Stuctural Db (CSD))
HSSP - Homology-derived secondary structure of proteins db
MutaProt - Comparison of PDB files which differ by point mutations
DisProt - Database of Protein Disorder
SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules

Proteomics databases and links
Gel-based data
MIAPEGelDB - A public repository for MIAPE Gel electrophoresis documents WORLD-2DPAGE List - Links to known 2-D PAGE database servers, as well as to 2-D PAGE related servers and services World-2DPAGE Repository - A public standards-compliant repository for gel-based proteomics data published in the literature The World-2DPAGE Constellation - Promote and publish gel-based proteomics data through the ExPASy server Proteomics Links page of the Swiss Proteomics Society
Mass spectrometry data
GPMdb - Global Proteome Machine Database OPD - Open Proteomics Database (currently down) PeptideAtlas - peptides identified in tandem mass spectrometry proteomics experiments PRIDE - PRoteomics IDEntifications database Tranche - Peer-to-peer distributed file system

Carbohydrates resources
FCCA - Forum Carbohydrates Coming of Age GlycoSuiteDB - Db of glycan structures Monosacharide browser - Space filling Fischer projection for monosaccharides genomics resource for animal lectins

Species specific databases:
Human
OMIM - Online Mendelian Inheritance in Man GENATLAS - Human genes atlas GeneTests - Medical genetics knowledge base GeneCards - Db integrating information on human genes GeneLoc - Integrated map of the human genome (ex- UDB) Ensembl Human genome browser The Gene Index Project - ex-TIGR Human Gene Indices Hs UniGene - Human transcripts in GenBank (EST clusters) STACK - Sequence Tag Alignment and Consensus Knowledgebase (Db of consensus human ESTs) Allgenes.org - Human predicted gene index/catalog GeneLynx - Portal to the human genome HUGE - Human Unidentified Gene-Encoded large proteins cDNA (KIAA...) CGAP - Cancer Genome Anatomy Project MGC - Mammalian Gene Collection SCDb - Stem cell db Homophila - Human Disease to Drosophila gene db Human Protein Atlas - Displays the expression and localization of proteins in a large variety of normal human tissues and cancer cells Progenetix CGH database - Molecular Cytogenetics in Leukemia and Cancer Contribution of the Sanger Centre to chromosomes 1,6,9,10,11,13,20,22 and X Chr1 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr2 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr3 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr4 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr5 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr6 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr7 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr8 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr9 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr10 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr11 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr12 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr13 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr14 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr15 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr16 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr17 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr18 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr19 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr20 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr21 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM Chr22 at HGC - Human genome center for chromosome 22 Chr22 UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM ChrX UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM ChrY UniProtKB/Swiss-Prot - entries, gene names and cross-references to MIM H-InvDB Database - Human gene db, with cDNA clones available from six high throughput cDNA sequencing projects Human Chromosome1 Launchpad Human Chromosome2 Launchpad Human Chromosome3 Launchpad Human Chromosome4 Launchpad Human Chromosome5 Launchpad Human Chromosome6 Launchpad Human Chromosome7 Launchpad Human Chromosome8 Launchpad Human Chromosome9 Launchpad Human Chromosome10 Launchpad Human Chromosome11 Launchpad Human Chromosome12 Launchpad Human Chromosome13 Launchpad Human Chromosome14 Launchpad Human Chromosome15 Launchpad Human Chromosome16 Launchpad Human Chromosome17 Launchpad Human Chromosome18 Launchpad Human Chromosome19 Launchpad Human Chromosome20 Launchpad Human Chromosome21 Launchpad Human Chromosome22 Launchpad Human ChromosomeX Launchpad Human ChromosomeY Launchpad
Vertebrates
OMIA - Online Mendelian Inheritance in Animals MGI - Mouse Genome Informatics (includes MGD) Ensembl Mouse genome browser DFCI MGI - TIGR Mouse Gene Index Mm UniGene - Mouse transcripts in GenBank (EST clusters) MGC - Mammalian Gene Collection Mouse gene knockouts db RGD - Rat genome db Ensembl Rat genome browser RatMAP - Rat genome db DFCI RGI - TIGR Rat Gene Index Rn Unigene - Rat transcripts in GenBank (EST clusters) Ensembl Chimpanzee genome browser Ensembl Gorilla genome browser Ensembl Cat genome browser Ensembl Bovine genome browser Ensembl Dog genome browser Ensembl Horse genome browser Ensembl Pig genome browser Ensembl Pig genome browser BOVMAP - Bovine genome db (in France) NHGRI Dog Genome Project ArkDB - Cat, Chicken, Cow, Deer, Horse, Pig, Quail, Sheep, Turkey genome databases Ensembl Chicken genome browser FishBase - Global information system on fishes Fugu genome project Fugu - HGMP Resource Centre Fugu Project (Fugu rubripes) Ensembl Fugu genome browser MEPD - Medaka Expression Pattern Database ArkDB - Sea Bass, Salmon genome databases ZFIN - Zebrafish Information Network Ensembl Zebrafish genome browser
Mitochondrion and chloroplast
GOBASE - Organelle Genome Database MitoDat - Mendelian Inheritance and the Mitochondrion db (mitochondrial nuclear gen C.caldarium - Cyanidium caldarium strain RK1 chloroplast genome
Insects
Drosophila UniProtKB/Swiss-Prot entries, gene names and cross-references to FlyBase FlyBase - Drosophila genetic and molecular db BDGP - Berkeley Drosophila Genome Project FlyView - Drosophila image db Homophila - Human Disease to Drosophila gene db AnoDB - Anopheles gambiae db Ensembl Anopheles gambiae genome browser
Invertebrates
WormBase - C.elegans db [Mirror at Sanger] C.elegans WWW server - at University of Texas Southwestern Ensembl C.elegans genome browser NEXTDB - The Nematode Expression Pattern DataBase C.elegans UniProtKB/Swiss-Prot entries, gene names and cross-references to WormPep WormPep - C.elegans proteins db WorfDB - C. elegans ORFeome cloning project Dictyostelium discoideum UniProtKB/Swiss-Prot entries, gene names and cross-references to DictyBase DictyBase - Dictyostelium discoideum db DictyDb - Dictyostelium discoideum db Dictyostelium Genome Sequencing project at BCM Cone shells Web site Parasite genomes db and resources PlasmoDB - P.falciparum genome db Malaria - WHO - Malaria db (from WHO) P.falciparum Sanger - P.falciparum genome project at Sanger P.falciparum - Plasmodium falciparum Gene Sequence Tag project Malaria parasite metabolic pathways GiardiaDB LGN - Leishmania major Genome Project ToxoDB - Toxoplasma gondii genome project Trypanosoma brucei genome project Trypanosoma cruzi genome project kDNA - Kinetoplast Minicircle Sequence db
Plants
NAL - AGIS - Access to many plant genome databases at the National Agricultural Library Mendel - Plant gene nomenclature database from CPGN FLAGdb++ - Integrative database around plant genomes Arabidopsis UniProtKB/Swiss-Prot entries, gene names and WWW servers TAIR - The Arabidopsis Information Resource MATDB - MIPS Arabidopsis thaliana db AMPL - Arabidopsis Membrane Protein Library Arabidopsis at PlaCe - Site with info on P450, glucosyltransferases, etc. Gramene - A comparative mapping resource for grains Oryza sativa UniProtKB/Swiss-Prot entries, gene names and WWW servers RGP - Rice Genome Research Program Oryzabase - Japanese rice genome db Rice genome annotation project - at MSU (Michigan State University) BeanGenes - Beans genome db Brassica Genome Gateway ChlamyDB - Chlamydomonas reinhardtii genome db CoffeeDNA - Coffee genomics web site CottonDB - Cotton genome db MaizeDb - Maize genome db Pisum sativum (pea) web site (in russian) TIGR Potato - TIGR Potato Functional Genomics project (at JCVI) Snapdragon (A.majus) web site DragonDB - Snapdragon Database SorghumDB - Sorghum genome db DFCI GmGI - DFCI Soybean Gene Index SoyBase - Soybean genome db SoyBase metabolic db - Metabolic subset of the soybean genome db DFCI LeGI - DFCI Tomato Gene Index Dendrome - Forest trees genome db
Fungi
Ensembl Yeast (S.cerevisiae) genome browser FGSC - Fungal Genetics Stock Center Genolevures - Genomic Exploration of the Hemiascomycete Yeasts FGI - Fungal genome initiative at the Broad Institute Fungal genome databases at MIPS Fungal genomes at the Sanger Institute FGR - Fungal Genome Resource MycoBank Yeast (S. cerevisiae) UniProtKB/Swiss-Prot entries, gene names and cross-references to SGD CYGD - MIPS Comprehensive Yeast Genome db SGD - Saccharomyces genome db Yeast snoRNA - Yeast small nucleolar RNAs db YTPdb - Yeast Transport Protein db YMPL - Yeast Membrane Protein Library YRC - Yeast Resource Center PROPHECY - PROfiling of PHEnotypic Characteristics in Yeast SCMD - Saccharomyces Cerevisiae Morphological db GPofYPF - Global Profiling of Yeast Protein Function Saccharomyces Genomes - Finding functional features in Saccharomyces Genomes by phylogenetic footprinting Yeast Comparative Genomics S.pombe UniProtKB/Swiss-Prot entries, gene names and WWW servers GeneDB S.Pombe - Schizosaccharomyces pombe GeneDB S.pombe genome project PombeNet - Forsburg lab pombe pages AGD - Ashbya genome db Aspergillus nidulans db The Aspergillus web site C. albicans UniProtKB/Swiss-Prot entries, gene names and WWW servers CGD - Candida Genome db C. albicans physical map - Candida albicans server at the Univ. of Minnesota Candida albicans pages - Candida albicans at the NRC/BRI CandidaDB - Candida albicans GenoList browser at Institut Pasteur Cryptococcus neoformans Genome Project FGDB - Fusarium graminearum Genome db Kluyveromyces lactis annotation db MNCDB - MIPS Neurospora crassa db Neurospora crassa db NGP - Neurospora crassa genome project at New Mexico Neurospora crassa Gene List MUMDB - MIPS Ustilago maydis db PC - Pneumocystis carinii genome project Phycomyces Web site - Resource site for scientists working on Phycomyces
Bacteria
WDCM - World Data Center for Microorganisms List of Bacterial Names with Standing in Nomenclature List of complete bacterial proteomes in Swiss-Prot (HAMAP) CBS - CBS Genome Atlas Database CMR - TIGR Comprehensive Microbial Ressource GIB - Genome information broker for Microbial genomes GOLD Genomes On-line Database HOBACGEN - Homologous Bacterial Genes db Comparison of the transport capabilities of bacterial genomes - from Ian Paulsen BPGD - Bacterial polysaccharide gene db Bacterial quorum sensing MicrobeWorld - Educational site on microbes E.coli UniProtKB/Swiss-Prot entries, gene names and cross-references to EcoGene EcoWeb / EcoGene - Very comprehensive E.coli db ECCE - E.coli Cell Envelope Protein Data Collection ECDC - E.coli db collection EcoCyc - Encyclopedia of E.coli genes and metabolism EchoBASE GenProtEC - E.coli genome and proteome db Colibri - E.coli GenoList browser at Institut Pasteur ECGC - E.coli Genome Center at Wisconsin University DDBJ E.coli - E.coli home page at DDBJ Regulon DB B.subtilis UniProtKB/Swiss-Prot entries, gene names and WWW servers SubtiList - Bacillus subtilis GenoList browser at Institut Pasteur NRSub - Bacillus subtilis non-redundant db DBTBS - Db of B.subtilis promoters and transcription factors A.actinomycetemcomitans - Actinobacillus actinomycetemcomitans strain HK1651 genome project B.stearothermophilus - Bacillus stearothermophilus strain 10 genome project Bordetella species genome projects at Sanger Institute - bronchiseptica strain RB50, parapertussis strain 1822 and pertussis strain Tohama I BbDB - Borrelia burgdorferi B31 genome db at JCVI-CMR Brucella abortus strain 2308 UniProtKB/Swiss-Prot entries, gene names and WWW servers Brucella abortus strain 9-941 UniProtKB/Swiss-Prot entries, gene names and WWW servers Brucella melitensis strain 16M UniProtKB/Swiss-Prot entries, gene names and WWW servers Brucella suis strain 1330 UniProtKB/Swiss-Prot entries, gene names and WWW servers B.aphidicola (subsp. Acyrthosiphon pisum) UniProtKB/Swiss-Prot entries, gene names and WWW servers B.aphidicola (subsp. Schizaphis graminum) UniProtKB/Swiss-Prot entries, gene names and WWW servers C.jejuni - Campylobacter jejuni genome project C.muridarum - Chlamydia muridarum strain MoPn genome db at JCVI-CMR C.pneumoniae AR39 - Chlamydia pneumoniae strain AR39 genome db at JCVI-CMR C.pneumoniae J138 - Chlamydia pneumoniae strain J138 genome db at JCVI-CMR Chromobacterium violaceum - Brazilian Genome C.michiganensis Claviabacter michiganensis subsp. sepdonicus genome project at Sanger Institute C.difficile - Clostridium difficile strain 630 genome project at Sanger Institute C.diphtheriae - Corynebacterium diphtheriae strain NCTC 13129 genome project at Sanger Institute Coxiella burnetii strain RSA 493 UniProtKB/Swiss-Prot entries, gene names and WWW servers CyanoBase - The Genome Database for Cyanobacteria CyanoList - Synechocystis PCC6803 and Anabaena PCC7120 GenoList browser at Institut Pasteur DrDB - Deinococcus radiodurans strain R1 genome db at JCVI-CMR E.ruminantium - Ehrlichia ruminantium (formerly Cowdria ruminantium) genome project at Sanger Institute H.influenzae UniProtKB/Swiss-Prot entries, gene names and WWW servers HiDB - Haemophilus influenzae genome db at JCVI-CMR H.pylori UniProtKB/Swiss-Prot entries, gene names and WWW servers HpDB - Helicobacter pylori strain 26695 genome db at JCVI-CMR PyloriGene - Helicobacter pylori GenoList browser at Institut Pasteur L.lactis - Lactobacillus lactis subsp. lactis strain IL1403 genome db L.plantarum - Lactobacillus plantarum genome project LegioList - Legionella pneumophila Paris strain and Legionella pneumophila Lens strain GenoList browser at Institut Pasteur ListiList - Listeria monocytogenes and Listeria innocua GenoList browser at Institut Pasteur BoviList - Mycobacterium bovis strain AF2122/97 GenoList browser at Institut Pasteur Mycobacterium - Mycobacterium genome projects at Sanger Institute Leproma - Mycobacterium leprae strain TN genome db TubercuList - Mycobacterium tuberculosis strain H37Rv GenoList browser at Institut Pasteur MtDB - Mycobacterium tuberculosis strain Oshkosh genome db at JCVI-CMR M.tuberculosis structural genomics consortium BuruList - Mycobacterium ulcerans strain Agy99 GenoList browser at Institut Pasteur M.genitalium UniProtKB/Swiss-Prot entries, gene names and WWW servers MgDB - Mycoplasma genitalium genome db at JCVI-CMR M.pneumoniae UniProtKB/Swiss-Prot entries, gene names and WWW servers M.pneumoniae - Mycoplasma pneumoniae genome project MypuList - Mycoplasma pulmonis GenoList browser at Institut Pasteur Mycoplasma synoviae genome db - Brazilian Genome Nesseria - Neisseria genome projects at Sanger Institute N.meningitidis B - Neisseria meningitidis serogroup B strain MC58 genome db at JCVI-CMR N.europaea - Nitrosomonas europaea genome project PhotoList - Photorhabdus luminescens strain TT01 GenoList browser at Institut Pasteur P.marinus - Prochlorococcus marinus genome project P.aeruginosa project - Pseudomonas aeruginosa genome project R.solanacearum - Ralstonia solanacearum genome project Rhizobium pNGR234a UniProtKB/Swiss-Prot entries, gene names and WWW servers RhizoBase - The Genome Database for Rhizobia Rhizobium pNGR234a analysis Rhodobacter sphaeroides genome db R.palustris - Rhodopseudomonas palustris genome project RicBase - Rickettsia conorii strain Malish 7 genome project R.bellii strain RML369-C UniProtKB/Swiss-Prot entries, gene names and WWW servers R.conorii strain Malish 7 UniProtKB/Swiss-Prot entries, gene names and WWW servers R.felis strain URRWXCa12 UniProtKB/Swiss-Prot entries, gene names and WWW servers R.prowazekii UniProtKB/Swiss-Prot entries, gene names and WWW servers R.typhi strain Wilmington UniProtKB/Swiss-Prot entries, gene names and WWW servers Salmonella - Salmonella genome projects at Sanger Institute S.meliloti - Sinorhizobium meliloti genome project AureoList - Staphylococcus aureus strains N315 and Mu50 GenoList browser at Institut Pasteur S.aureus - Staphylococcus aureus strain NCTC 8325 genome project SagaList - Streptococcus agalactiae strain NEM316 GenoList browser at Institut Pasteur StreptoPneumoList - Streptococcus pneumoniae strains R6 and Tigr4 GenoList browser at Institut Pasteur S.mutans - Streptococcus mutans strain UAB159 genome project S.pyogenes M1 - Streptococcus pyogenes strain SF370 serotype M1 genome project S.pyogenes - Streptococcus pyogenes genome project at Sanger Institute S.suis - Streptococcus suis genome project at Sanger Institute S.uberis - Streptococcus uberis genome project at Sanger Institute S.coelicolor - Streptomyces coelicolor genome project at Sanger Institute S.avermitilis - Streptomyces avermitilis strain MA-4680 genome project Synechocystis strain PCC 6803 UniProtKB/Swiss-Prot entries, gene names and WWW servers TmDB - Thermotoga maritima genome db at JCVI-CMR TpDB - Treponema pallidum genome db at JCVI-CMR T.whipplei - Tropheryma whipplei genome project at Sanger Institute U.urealyticum - Ureaplasma urealyticum genome WWW site VcDB - Vibrio cholerae genome db at JCVI-CMR X.fastidiosa - Xylella fastidiosa genome project Yersinia - Yersinia genome projects at Sanger Institute
Archaea
List of complete archaeal proteomes in Swiss-Prot (HAMAP) UCSC Archeal Genome Browser A.pernix - Aeropyrum pernix K1 genome db AfDB - Archaeoglobus fulgidus genome db at JCVI-CMR Halobacterium NRC-1 - Halobacterium strain NRC-1 genome project M.jannaschii UniProtKB/Swiss-Prot entries, gene names and WWW servers MjDB - Methanococcus jannaschii genome db at JCVI-CMR Pyrococcus abyssi genome and re-annotation db Pyrococcus sp. OT3 Sulfolobus solfataricus P2 genome project T.volcanium - Thermoplasma volcanium genome project
Viruses and phages
All the virology on the WWW - links to virology WWW servers by David M. Sander ICTVdB - Universal virus taxonomy db ViralZone - Portal to viral UniProtKB/Swiss-Prot entries Adenoviruses web site HCVDB - Hepatitis C virus db HIV - HIV and related species db HPV - Human papillomaviruses db Picornavirus - Picornavirus home page and access to db VirOligo- virus-specific oligonucleotides database PhageBase Phage Sequence Databank at Sdsu Center for Universal Microbial Sequencing (currently not working) The Bacteriophage Ecology Group GOLD - Genomes On-line db DOGS - Database of genome sizes

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