Bioinformatics databases links

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Note: The following list was inspired by databases cross-referenced in UniProtKB/Swiss-Prot.

  • AGD
Name  : Ashbya genome database
Ref  : BMC Genomics 8:9-9(2007); PubMed:17212814 ; DOI:10.1186/1471-2164-8-9 ;
LinkTp: Explicit
Server: http://agd.vital-it.ch/
Db_URL: http://agd.vital-it.ch/Ashbya_gossypii/geneview?gene=%s
Cat  : Organism-specific gene databases
  • ANU-2DPAGE
Name  : Australian National University 2-DE database
Ref  : Proteomics 1:1149-1161(2001); PubMed:11990509 ; DOI:<1149::AID-PROT1149>3.0.CO;2-R 10.1002/1615-9861(200109)1:9<1149::AID-PROT1149>3.0.CO;2-R ;
LinkTp: Explicit
Server: http://semele.anu.edu.au
Cat  : 2D gel databases
  • AraC-XylS
Name  : AraC-XylS; a database on a family of Helix-Turn-Helix transcription factors from bacteria
Ref  : Nucleic Acids Res. 30:318-321(2002); PubMed:11752325 ;
LinkTp: Implicit; All bacterial Swiss-Prot entries with a cross-reference to PROSITE PS01124
Server: http://www.eez.csic.es/arac-xyls/
Db_URL: http://www.eez.csic.es/arac-xyls/wfichas/%s.HTM
Cat  : Protein family/group databases
  • ArrayExpress
Name  : ArrayExpress repository for microarray data
Ref  : Nucleic Acids Res. 35:D747-D750(2007); PubMed:17132828 ; DOI:10.1093/nar/gkl995 ;
LinkTp: Explicit
Server: http://www.ebi.ac.uk/arrayexpress/
Db_URL: http://www.ebi.ac.uk/aedw/dwd?uniprot=%s
Cat  : Gene expression databases
  • BioCyc
Name  : Collection of Pathway/Genome Databases
Ref  : Nucleic Acids Res. 33:6083-6089(2005); PubMed:16246909 ; DOI:10.1093/nar/gki892 ;
LinkTp: Explicit
Server: http://www.biocyc.org/
Db_URL: http://biocyc.org/getid?id=%s
Cat  : Enzyme and pathway databases
  • BLOCKS
Name  : BLOCKS; a protein domain database
Ref  : Nucleic Acids Res. 28:228-230(2000); PubMed:10592233 ;
LinkTp: Implicit; All Swiss-Prot entries
Server: http://blocks.fhcrc.org/
Db_URL: http://blocks.fhcrc.org/blocks-bin/getblock.sh?%s
Cat  : Family and domain databases
  • BuruList
Name  : Mycobacterium ulcerans genome database
LinkTp: Explicit
Server: http://genolist.pasteur.fr/BuruList/
Cat  : Organism-specific gene databases
  • CleanEx
Name  : CleanEx database of gene expression profiles
Ref  : Nucleic Acids Res. 32:D542-D547(2004); PubMed:14681477 ; DOI:10.1093/nar/gkh107 ;
LinkTp: Implicit; all human and mouse entries with >= HGNC or MGI X-ref
Server: http://www.cleanex.isb-sib.ch/
Db_URL: http://www.cleanex.isb-sib.ch/cgi-bin/cleanex_query_result.pl?out_format=NICE&Entry_0=HGNC:%s
Cat  : Gene expression databases
  • CMR
Name  : Comprehensive Microbial Resource
LinkTp: Implicit; all entries from completely sequenced microbial genomes which don't have an explicit link to TIGR
Server: http://http://cmr.tigr.org/
Cat  : Genome annotation databases
  • COMPLUYEAST-2DPAGE
Name  : 2-DE database at Universidad Complutense de Madrid
Ref  : J. Chromatogr. B. Biomed. Sci. Appl. 787:129-148(1993); PubMed:12659738 ;
LinkTp: Explicit
Server: http://babbage.csc.ucm.es/2d/2d.html
Cat  : 2D gel databases
  • Cornea-2DPAGE
Name  : Human Cornea 2-DE database
LinkTp: Explicit
Server: http://www.cornea-proteomics.com/
Db_URL: http://www.daimi.au.dk/cgi-jje/2d/2d.cgi?ac=%s&database=cornea
Cat  : 2D gel databases
  • Cyclebase
Name  : Cyclebase
Server: http://cyclebase.org/
  • CYGD
Name  : Comprehensive Yeast Genome Database
Ref  : Nucleic Acids Res. 33:D364-D368(2005); PubMed:15608217 ; DOI:10.1093/nar/gki053 ;
LinkTp: Explicit
Server: http://mips.gsf.de/genre/proj/yeast
Db_URL: http://mips.gsf.de/genre/proj/yeast/singleGeneReport.html?entry=%s
Cat  : Organism-specific gene databases
  • dbSNP
Name  : Database of single nucleotide polymorphism
Ref  : Nucleic Acids Res. 35:D5-12(2007); PubMed:17170002 ; DOI:10.1093/nar/gkl1031 ;
LinkTp: Explicit
Server: http://www.ncbi.nlm.nih.gov/SNP/
Db_URL: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s
Cat  : Polymorphism databases
  • DDBJ
Name  : DNA Data Bank of Japan; a nucleotide sequence database
Ref  : Nucleic Acids Res. 35:D13-D15(2007); PubMed:17108353 ; DOI:10.1093/nar/gkl908 ;
LinkTp: Implicit; All Swiss-Prot entries with >=1 EMBL Xref.
Server: http://www.ddbj.nig.ac.jp/
Cat  : Sequence databases
  • DictyBase
Name  : Dictyostelium discoideum online informatics resource
Ref  : Nucleic Acids Res. 34:D423-D427(2006); PubMed:16381903 ; DOI:10.1093/nar/gkj090 ;
LinkTp: Explicit
Server: http://dictybase.org/
Db_URL: http://dictybase.org/db/cgi-bin/dictyBase/locus.pl?locus=%s
Cat  : Organism-specific gene databases
  • DIP
Name  : Database of interacting proteins
Ref  : Nucleic Acids Res. 32:D449-D451(2004); PubMed:14681454 ; DOI:10.1093/nar/gkh086 ;
LinkTp: Explicit
Server: http://dip.doe-mbi.ucla.edu/
Db_URL: http://dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=%s
Cat  : Protein-protein interaction databases
  • DOSAC-COBS-2DPAGE
Name  : DOSAC-COBS 2D-PAGE database
LinkTp: Explicit
Server: http://www.dosac.unipa.it/2d/
Db_URL: http://www.dosac.unipa.it/cgi-bin/2d/2d.cgi?ac=%s
Cat  : 2D gel databases
  • DrugBank
Name  : Drug and drug target database
Ref  : Nucleic Acids Res. 34:D668-D672(2006); PubMed:16381955 ; DOI:10.1093/nar/gkj067 ;
LinkTp: Explicit
Server: http://redpoll.pharmacy.ualberta.ca/drugbank/
Db_URL: http://redpoll.pharmacy.ualberta.ca/drugbank/cgi-bin/getCard.cgi?CARD=%s.txt
Cat  : Other
  • EchoBASE
Name  : EchoBASE - an integrated post-genomic database for E. coli
Ref  : Nucleic Acids Res. 33:D329-D333(2005); PubMed:15608209 ; DOI:10.1093/nar/gki028 ;
LinkTp: Explicit
Server: http://www.biolws1.york.ac.uk/echobase/
Db_URL: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=%s
Cat  : Organism-specific gene databases
  • EcoGene
Name  : Escherichia coli strain K12 genome database
Ref  : Nucleic Acids Res. 28:60-64(2000); PubMed:10592181 ;
LinkTp: Explicit
Server: http://www.ecogene.org/
Db_URL: http://www.ecogene.org/geneInfo.php?eg_id=%s
Cat  : Organism-specific gene databases
  • EMBL
Name  : EMBL nucleotide sequence database
Ref  : Nucleic Acids Res. 35:D16-D20(2007); PubMed:17148479 ; DOI:10.1093/nar/gkl913 ;
LinkTp: Explicit
Server: http://www.ebi.ac.uk/embl/
Db_URL: http://www.ebi.ac.uk/htbin/expasyfetch?%s
Cat  : Sequence databases
  • Ensembl
Name  : Ensembl eukaryotic genome annotation project
Ref  : Nucleic Acids Res. 35:D610-D617(2007); PubMed:17148474 ; DOI:10.1093/nar/gkl996 ;
LinkTp: Explicit
Server: http://www.ensembl.org/
Cat  : Genome annotation databases
  • ENZYME
Name  : Enzyme nomenclature database
Ref  : Nucleic Acids Res. 28:304-305(2000); PubMed:10592255 ;
LinkTp: Implicit; All Swiss-Prot entries that contain >=1 EC numbers in their description lines
Server: http://www.expasy.org/enzyme/
Cat  : Enzyme and pathway databases
  • euHCVdb
Name  : European Hepatitis C Virus database
Ref  : Nucleic Acids Res. 35:D363-D366(2007); PubMed:17142229 ; DOI:10.1093/nar/gkl970 ;
LinkTp: Explicit
Server: http://euhcvdb.ibcp.fr/euHCVdb/
Db_URL: http://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=%s
Cat  : Organism-specific gene databases
  • FlyBase
Name  : Drosophila genome database
Ref  : Nucleic Acids Res. 35:D486-D491(2007); PubMed:17099233 ; DOI:10.1093/nar/gkl827 ;
LinkTp: Explicit
Server: http://flybase.bio.indiana.edu/
Db_URL: http://flybase.bio.indiana.edu/.bin/fbidq.html?%s
Note  : Obsolete abbreviation: DMAP
Cat  : Organism-specific gene databases
  • FlyTF
Name  : The Drosophila Transcription Factor Database
Ref  : Bioinformatics 22(12):1532-1533(2006); DOI:10.1093/bioinformatics/btl143
Server: http://www.flytf.org/
  • GenAtlas
Name  : GenAtlas: human gene database
Ref  : C. R. Acad. Sci. III, Sci. Vie 321:805-817(1998); PubMed:9835018 ;
LinkTp: Implicit; Human sequence entries with >=1 gene name and >=1 HGNC X-ref.
Server: http://www.dsi.univ-paris5.fr/genatlas/
Db_URL: http://www.dsi.univ-paris5.fr/genatlas/fiche.php?symbol=%s
Cat  : Organism-specific gene databases
  • GenBank
Name  : GenBank nucleotide sequence database
Ref  : Nucleic Acids Res. 35:D5-12(2007); PubMed:17170002 ; DOI:10.1093/nar/gkl1031 ;
LinkTp: Implicit; All Swiss-Prot entries with >=1 EMBL Xref.
Server: http://www.ncbi.nlm.nih.gov/
Cat  : Sequence databases
  • Gene3D
Name  : Gene3D Structural and Functional Annotation of Protein Families
Ref  : Nucleic Acids Res. 34:D281-D284(2006); PubMed:16381865 ; DOI:10.1093/nar/gkj057 ;
LinkTp: Explicit
Server: http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
Db_URL: http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/GotoCath.pl?cath=%s
Cat  : Family and domain databases
  • GeneCards
Name  : GeneCards: human genes, protein and diseases
Ref  : Bioinformatics 18:1542-1543(2002); PubMed:12424129 ;
LinkTp: Implicit; Human sequence entries with >=1 gene name and >=1 HGNC X-ref.
Server: http://www.genecards.org/
Db_URL: http://www.genecards.org/cgi-bin/carddisp?%s
Cat  : Organism-specific gene databases
  • GeneDB_Spombe
Name  : Schizosaccharomyces pombe GeneDB
Ref  : Nucleic Acids Res. 32:D339-D343(2004); PubMed:14681429 ; DOI:10.1093/nar/gkh007 ;
LinkTp: Explicit
Server: http://www.genedb.org/genedb/pombe/
Db_URL: http://www.genedb.org/genedb/Search?submit=Search+for&name=%s&organism=pombe&desc=yes
Cat  : Organism-specific gene databases
  • GeneFarm
Name  : Structural and functional annotation of Arabidopsis thaliana gene and protein families.
Ref  : Nucleic Acids Res. 33:D641-D646(2005); PubMed:15608279 ; DOI:10.1093/nar/gki115 ;
LinkTp: Explicit
Server: http://urgi.versailles.inra.fr/Genefarm/index.htpl
Db_URL: http://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=%s
Cat  : Organism-specific gene databases
  • GeneLynx
Name  : GeneLynx; a portal to the human, mouse and rat genomes
Ref  : Genome Res. 11:2151-2157(2001); PubMed:11731507 ; DOI:10.1101/gr.199801 ;
LinkTp: Implicit; Human sequence entries with >=1 gene name and >=1 HGNC X-ref or mouse sequence with >=1 MGI X-ref or rat sequence with >=1 RGD X-ref.
Server: http://www.genelynx.org/
Cat  : Organism-specific gene databases
  • GenomeReviews
Name  : Genome Reviews; an annotated view of completely sequenced genomes
Ref  : Nucleic Acids Res. 33:D297-D302(2005); PubMed:15608201 ; DOI:10.1093/nar/gki039 ;
LinkTp: Explicit
Server: http://www.ebi.ac.uk/GenomeReviews/
Cat  : Genome annotation databases
  • GermOnline
Name  : GermOnline - a gateway for gametogenesis
Ref  : Nucleic Acids Res. 35:D457-D462(2007); PubMed:17145711 ; DOI:10.1093/nar/gkl957 ;
LinkTp: Explicit
Server: http://www.germonline.org/
Db_URL: http://www.germonline.org/%s/geneview?gene=%s
Cat  : Gene expression databases
  • GlycoSuiteDB
Name  : GlycoSuiteDB; an annotated and curated relational database of glycan structures
Ref  : Nucleic Acids Res. 31:511-513(2003); PubMed:12520065 ;
LinkTp: Explicit
Server: https://tmat.proteomesystems.com/glycosuite/
Cat  : PTM databases
  • GO
Name  : Gene Ontology
Ref  : Nucleic Acids Res. 34:D322-D326(2006); PubMed:16381878 ; DOI:10.1093/nar/gkj021 ;
LinkTp: Explicit
Server: http://www.geneontology.org/
Db_URL: http://www.ebi.ac.uk/ego/QuickGO?mode=display&entry=%s
Cat  : Ontologies
  • GPCRDB
Name  : Information system for G protein-coupled receptors (GPCRs)
Ref  : Nucleic Acids Res. 29:346-349(2001); PubMed:11125133 ;
LinkTp: Implicit; All Swiss-Prot entries that contains a CC line of the type: "-!- SIMILARITY: Belongs to the G-protein coupled receptor ..."
Server: http://www.gpcr.org/7tm/
Cat  : Protein family/group databases
  • Gramene
Name  : Gramene; a comparative mapping resource for grains
Ref  : Nucleic Acids Res. 34:D717-D723(2006); PubMed:16381966 ; DOI:10.1093/nar/gkj154 ;
LinkTp: Explicit
Server: http://www.gramene.org/
Db_URL: http://www.gramene.org//db/protein/protein_search?acc=%s
Cat  : Organism-specific gene databases
  • H-InvDB
Name  : H-Invitational Database, human transcriptome db
Ref  : Gene 364:99-107(2005); PubMed:16185827 ; DOI:10.1016/j.gene.2005.05.036 ;
LinkTp: Explicit
Server: http://www.h-invitational.jp/
Db_URL: http://www.jbirc.aist.go.jp/hinv/soup/pub_Locus.pl?locus_id=%s
Cat  : Organism-specific gene databases
  • HAMAP
Name  : HAMAP database of microbial protein families
Ref  : Comput. Biol. Chem. 27:49-58(2003); PubMed:12798039 ;
LinkTp: Explicit
Server: http://www.expasy.org/sprot/hamap/
Db_URL: http://www.expasy.org/cgi-bin/hamap/nicemf.cgi?%s
Cat  : Family and domain databases
  • HGNC
Name  : Human Gene Nomenclature Database
Ref  : Nucleic Acids Res. 34:D319-D321(2006); PubMed:16381876 ; DOI:10.1093/nar/gkj147 ;
LinkTp: Explicit
Server: http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl
Db_URL: http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/get_data.pl?hgnc_id=%s
Note  : Obsolete abbreviation: Genew
Cat  : Organism-specific gene databases
  • HIV
Name  : HIV sequence database
LinkTp: Explicit
Server: http://www.hiv.lanl.gov/content/hiv-db/mainpage.html
Cat  : Organism-specific gene databases
  • HOGENOM
Name  : Homologous Sequences from Complete Genomes database
LinkTp: Implicit; entries from Bacteria and Archaea except fragments of <100 AA
Server: http://pbil.univ-lyon1.fr/databases/hogenom.html
Db_URL: http://pbil.univ-lyon1.fr/cgi-bin/acnuc-link-ac2fam?db=Hogenprot&query=%s
Cat  : Organism-specific gene databases
  • HOVERGEN
Name  : Homologous vertebrate genes database
Ref  : Nucleic Acids Res. 22:2360-2365(1994); PubMed:8036164 ;
LinkTp: Implicit; entries from Vertebrata except fragments of <100 AA
Server: http://pbil.univ-lyon1.fr/databases/hovergen.html
Db_URL: http://pbil.univ-lyon1.fr/cgi-bin/acnuc-link-ac2fam?db=Hoverprot&query=%s
Cat  : Organism-specific gene databases
  • HPA
Name  : Human Protein Atlas
Ref  : Mol. Cell. Proteomics 4:1920-1932(2005); PubMed:16127175 ; DOI:10.1074/mcp.M500279-MCP200 ;
LinkTp: Explicit
Server: http://www.proteinatlas.org/
Db_URL: http://www.proteinatlas.org/tissue_profile.php?antibody_id=%s
Cat  : Organism-specific gene databases
  • HSC-2DPAGE
Name  : 2-DE gel protein databases at Harefield
Ref  : Electrophoresis 18:471-479(1997); PubMed:9150926 ;
LinkTp: Explicit
Server: http://www.doc.ic.ac.uk/vip/hsc-2dpage/
Cat  : 2D gel databases
  • HSSP
Name  : Homology-derived secondary structure of proteins database
Ref  : Nucleic Acids Res. 27:244-247(1999); PubMed:9847191 ;
LinkTp: Explicit
Server: http://www.sander.ebi.ac.uk/hssp/
Db_URL: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e
Cat  : 3D structure databases
  • HUGE
Name  : Human Unidentified Gene-Encoded large proteins database
Ref  : Nucleic Acids Res. 32:D502-D504(2004); PubMed:14681467 ; DOI:10.1093/nar/gkh035 ;
LinkTp: Implicit; Human sequence entries with KIAAnnnn in a GN line
Server: http://www.kazusa.or.jp/huge/
Cat  : Organism-specific gene databases
  • IMGT
Name  : ImMunoGeneTics db
Ref  : Nucleic Acids Res. 34:D781-D784(2006); PubMed:16381979 ; DOI:10.1093/nar/gkj088 ;
LinkTp: Implicit; All entries with a KW "Immunoglobulin [CV] region" and >=1 EMBL X-ref.
Server: http://imgt.cines.fr/
Cat  : Protein family/group databases
  • IntAct
Name  : Protein interaction database and analysis system
Ref  : Nucleic Acids Res. 35:D561-D565(2007); PubMed:17145710 ; DOI:10.1093/nar/gkl958 ;
LinkTp: Explicit
Server: http://www.ebi.ac.uk/intact/
Db_URL: http://www.ebi.ac.uk/intact/search/do/hvWelcome?searchClass=Interactor&searchString=%s
Cat  : Protein-protein interaction databases
  • InterPro
Name  : Integrated resource of protein families, domains and functional sites
Ref  : Nucleic Acids Res. 35:D224-D228(2007); PubMed:17202162 ; DOI:10.1093/nar/gkl841 ;
LinkTp: Explicit
Server: http://www.ebi.ac.uk/interpro/
Db_URL: http://www.ebi.ac.uk/interpro/IEntry?ac=%s
Cat  : Family and domain databases
  • KEGG
Name  : KEGG: Kyoto Encyclopedia of Genes and Genomes
Ref  : Nucleic Acids Res. 34:D354-D357(2006); PubMed:16381885 ; DOI:10.1093/nar/gkj102 ;
LinkTp: Explicit
Server: http://www.genome.jp/kegg/
Db_URL: http://www.genome.jp/dbget-bin/www_bget?%s
Cat  : Genome annotation databases
  • LegioList
Name  : Legionella pneumophila genome database
Ref  : BMC Genomics 6:14-14(2005); PubMed:15698474 ; DOI:10.1186/1471-2164-6-14 ;
LinkTp: Explicit
Server: http://genolist.pasteur.fr/LegioList/
Cat  : Organism-specific gene databases
  • Leproma
Name  : Mycobacterium leprae genome database
LinkTp: Explicit
Server: http://genolist.pasteur.fr/Leproma/
Cat  : Organism-specific gene databases
  • LinkHub
Name  : LinkHub; links to different genomics and protein resources
LinkTp: Explicit
Server: http://hub.gersteinlab.org/
Db_URL: http://hub.gersteinlab.org/id/%s/link_origin/UNIPROT
Cat  : Other
  • ListiList
Name  : Listeria innocua and Listeria monocytogenes genomes database
LinkTp: Explicit
Server: http://genolist.pasteur.fr/ListiList/
Cat  : Organism-specific gene databases
  • MaizeGDB
Name  : Maize Genetics and Genomics Database
Ref  : Nucleic Acids Res. 35:D895-D900(2007); PubMed:17202174 ; DOI:10.1093/nar/gkl1048 ;
LinkTp: Explicit
Server: http://www.maizegdb.org/
Db_URL: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=%s
Note  : Obsolete abbreviation: MaizeDB
Cat  : Organism-specific gene databases
  • MEROPS
Name  : MEROPS protease database
Ref  : Nucleic Acids Res. 34:D270-D272(2006); PubMed:16381862 ; DOI:10.1093/nar/gkj089 ;
LinkTp: Explicit
Server: http://merops.sanger.ac.uk/
Db_URL: http://merops.sanger.ac.uk/cgi-bin/make_frame_file?id=%s
Cat  : Protein family/group databases
  • MGI
Name  : Mouse genome database (MGD) from Mouse Genome Informatics (MGI)
Ref  : Nucleic Acids Res. 35:D630-D637(2007); PubMed:17135206 ; DOI:10.1093/nar/gkl940 ;
LinkTp: Explicit
Server: http://www.informatics.jax.org/
Db_URL: http://www.informatics.jax.org/searches/accession_report.cgi?id=%s
Note  : Obsolete abbreviation: MGD
Cat  : Organism-specific gene databases
  • Micado
Name  : Microbial advanced database
LinkTp: Implicit; All Swiss-Prot entries with >=1 SubtiList Xref where the gene name does not start with "Y"
Server: http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi
Db_URL: http://genome.jouy.inra.fr/micado/gene.cgi?species=Bacillus+subtilis&gene=%2
Cat  : Organism-specific gene databases
  • MIM
Name  : Online Mendelian Inheritance in Man (OMIM)
Ref  : Nucleic Acids Res. 33:D514-D517(2005); PubMed:15608251 ; DOI:10.1093/nar/gki033 ;
LinkTp: Explicit
Server: http://www.ncbi.nlm.nih.gov/omim/
Db_URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=OMIM&dopt=Detailed&tmpl=dispomimTemplate&list_uids=%s
Cat  : Organism-specific gene databases
  • ModBase
Name  : Database of comparative protein structure models
Ref  : Nucleic Acids Res. 34:D291-D295(2006); PubMed:16381869 ; DOI:10.1093/nar/gkj059 ;
LinkTp: Implicit; All Swiss-Prot and TrEMBL entries
Server: http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi
Cat  : 3D structure databases
  • MypuList
Name  : Mycoplasma pulmonis genome database
LinkTp: Explicit
Server: http://genolist.pasteur.fr/MypuList/
Cat  : Organism-specific gene databases
  • NIEHS-SNPs
Name  : NIEHS SNPs Program at the University of Washington
LinkTp: Implicit; all entries with >= HGNC X-ref and an RT line starting with "NIEHS-SNPs"
Server: http://egp.gs.washington.edu/
Db_URL: http://egp.gs.washington.edu/data/%s/
Cat  : Polymorphism databases
  • NucleaRDB
Name  : Information system for nuclear receptors
Ref  : Nucleic Acids Res. 29:346-349(2001); PubMed:11125133 ;
LinkTp: Implicit; All Swiss-Prot entries that contain a CC line of the type: "-!- SIMILARITY: Belongs to the nuclear hormone receptor family."
Server: http://www.receptors.org/NR/
Cat  : Protein family/group databases
  • OGP
Name  : Oxford GlycoProteomics 2-DE database, Oxford University, England
LinkTp: Explicit
Server: http://proteomewww.bioch.ox.ac.uk/2d/2d.html
Db_URL: http://proteomewww.bioch.ox.ac.uk/cgi-bin/get-2d-entry?%s
Cat  : 2D gel databases
  • Orphanet
Name  : Orphanet; a database dedicated to information on rare diseases and orphan drugs
Server: http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB
Db_URL: http://www.orpha.net//consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=%s
Cat  : Organism-specific gene databases
  • PANTHER
Name  : The PANTHER Classification System
Ref  : Nucleic Acids Res. 35:D247-D252(2007); PubMed:17130144 ; DOI:10.1093/nar/gkl869 ;
LinkTp: Explicit
Server: http://www.pantherdb.org/
Db_URL: http://www.pantherdb.org/panther/family.do?clsAccession=%s
Cat  : Family and domain databases
  • PDB
Name  : The RCSB Protein Data Bank; a repository for 3D biological macromolecular structure data
Ref  : Nucleic Acids Res. 34:D302-D305(2006); PubMed:16381872 ; DOI:10.1093/nar/gkj120 ;
LinkTp: Explicit
Server: http://www.rcsb.org/pdb/
Db_URL: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e
Cat  : 3D structure databases
  • PeroxiBase
Name  : PeroxiBase, a plant peroxidase database
LinkTp: Explicit
Server: http://peroxidase.isb-sib.ch/index.php
Db_URL: http://peroxidase.isb-sib.ch/listing.php?action=view&id=%s
Cat  : Protein family/group databases
  • Pfam
Name  : Pfam protein domain database
Ref  : Nucleic Acids Res. 34:D247-D251(2006); PubMed:16381856 ; DOI:10.1093/nar/gkj149 ;
LinkTp: Explicit
Server: http://www.sanger.ac.uk/Software/Pfam/ ~OR~ http://pfam.wustl.edu/
Db_URL: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?%s
Cat  : Family and domain databases
  • PHCI-2DPAGE
Name  : Parasite host cell interaction 2D-PAGE database
LinkTp: Explicit
Server: http://www.gram.au.dk/2d/2d.html
Cat  : 2D gel databases
  • PhosSite
Name  : Phosphorylation site database for Archaea and Bacteria
LinkTp: Explicit
Server: http://vigen.biochem.vt.edu/xpd/xpd.htm
Db_URL: http://vigen.biochem.vt.edu/xpd/xpd2.cfm?extf=swissprot&extref=%s
Cat  : PTM databases
  • PhotoList
Name  : Photorhabdus luminescens genome database
LinkTp: Explicit
Server: http://genolist.pasteur.fr/PhotoList/
Cat  : Organism-specific gene databases
  • PIR
Name  : Protein sequence database of the Protein Information Resource
LinkTp: Explicit
Server: http://pir.georgetown.edu/
Db_URL: http://pir.georgetown.edu/cgi-bin/nbrfget?uid=%s
Cat  : Sequence databases
  • PIRSF
Name  : PIR superfamilies, an integrated protein classification database
Ref  : Nucleic Acids Res. 32:D112-D114(2004); PubMed:14681371 ; DOI:10.1093/nar/gkh097 ;
LinkTp: Explicit
Server: http://pir.georgetown.edu/iproclass/
Db_URL: http://pir.georgetown.edu/cgi-bin/ipcSF?id=%s
Cat  : Family and domain databases
  • PMMA-2DPAGE
Name  : Purkyne Military Medical Academy 2D-PAGE database
LinkTp: Explicit
Server: http://www.pmma.pmfhk.cz/2d/2d.html
Cat  : 2D gel databases
  • PptaseDB
Name  : Prokaryotic Protein Phosphatase Database
LinkTp: Explicit
Server: http://vigen.biochem.vt.edu/p3d/p3d.htm
Db_URL: http://vigen.biochem.vt.edu/p3d/p3d2.cfm?extf=accession&extref=%s
Cat  : Protein family/group databases
  • PRINTS
Name  : Protein Motif fingerprint database; a protein domain database
Ref  : Nucleic Acids Res. 31:400-402(2003); PubMed:12520033 ;
LinkTp: Explicit
Server: http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
Db_URL: http://umber.sbs.man.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=%s
Note  : Obsolete abbreviation: PRINT
Cat  : Family and domain databases
  • ProDom
Name  : ProDom; a protein domain database
Ref  : Nucleic Acids Res. 33:D212-D215(2005); PubMed:15608179 ; DOI:10.1093/nar/gki034 ;
LinkTp: Explicit
Server: http://prodom.prabi.fr/prodom/current/html/home.php
Db_URL: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=SPTR&query=%s
Cat  : Family and domain databases
  • PROSITE
Name  : PROSITE; a protein domain and family database
Ref  : Nucleic Acids Res. 34:D227-D230(2006); PubMed:16381852 ; DOI:10.1093/nar/gkj063 ;
LinkTp: Explicit
Server: http://www.expasy.org/prosite/
Db_URL: http://www.expasy.org/cgi-bin/get-prosite-raw.pl?%s
Cat  : Family and domain databases
  • ProtoNet
Name  : ProtoNet; Automatic hierarchical classification of proteins
Ref  : Protein Sci. 15:1557-1562(2006); PubMed:16672244 ; DOI:10.1110/ps.062185706 ;
LinkTp: Implicit; All Swiss-Prot entries
Server: http://www.protonet.cs.huji.ac.il/
Db_URL: http://www.protonet.cs.huji.ac.il/protonet/sp.jsp?prot=%s
Cat  : Other
  • PseudoCAP
Name  : Pseudomonas genome database
Ref  : Nucleic Acids Res. 33:D338-D343(2005); PubMed:15608211 ; DOI:10.1093/nar/gki047 ;
LinkTp: Explicit
Server: http://www.pseudomonas.com/
Db_URL: http://www.pseudomonas.com/getAnnotation.do?locusID=%s
Cat  : Organism-specific gene databases
  • Rat-heart-2DPAGE
Name  : 2-DE database of rat heart, at German Heart Institute Berlin, Germany
Ref  : Electrophoresis 20:891-897(1999); PubMed:10344264 ;
LinkTp: Explicit
Server: http://www.mpiib-berlin.mpg.de/2D-PAGE/RAT-HEART/2d/
Db_URL: http://www.mpiib-berlin.mpg.de/mpiib-cgi/RAT-HEART/get-2d-entry?%s
Cat  : 2D gel databases
  • Reactome
Name  : Reactome - a knowledgebase of biological pathways and processes
Ref  : Nucleic Acids Res. 33:D428-D432(2005); PubMed:15608231 ; DOI:10.1093/nar/gki072 ;
LinkTp: Explicit
Server: http://www.reactome.org/
Db_URL: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=%s
Note  : Obsolete abbreviation: GK
Cat  : Enzyme and pathway databases
  • REBASE
Name  : Restriction enzymes and methylases database
Ref  : Nucleic Acids Res. 35:D269-D270(2007); PubMed:17202163 ; DOI:10.1093/nar/gkl891 ;
LinkTp: Explicit
Server: http://rebase.neb.com/
Db_URL: http://rebase.neb.com/rebase/enz/%s.html
Cat  : Protein family/group databases
  • REPRODUCTION-2DPAGE
Name  : REPRODUCTION-2DPAGE
LinkTp: Explicit
Server: http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi
Db_URL: http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=?%s
Cat  : 2D gel databases
  • RGD
Name  : Rat genome database
Ref  : Nucleic Acids Res. 35:D658-D662(2007); PubMed:17151068 ; DOI:10.1093/nar/gkl988 ;
LinkTp: Explicit
Server: http://rgd.mcw.edu/
Db_URL: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=%s
Cat  : Organism-specific gene databases
  • Rouge
Name  : Rodent Unidentified Gene-Encoded large proteins database
Ref  : Nucleic Acids Res. 32:D502-D504(2004); PubMed:14681467 ; DOI:10.1093/nar/gkh035 ;
LinkTp: Implicit; Mouse sequence entries with KIAAnnnn in a GN line
Server: http://www.kazusa.or.jp/rouge/
Cat  : Organism-specific gene databases
  • RZPD-ProtExp
Name  : RZPDs collection of validated ORF protein expression clones
LinkTp: Explicit
Server: http://www.rzpd.de/products/orfclones/
Db_URL: http://www.rzpd.de/gene?productId=%s
Cat  : Other
  • SagaList
Name  : Streptococcus agalactiae NEM316 / Serotype III genome database
LinkTp: Explicit
Server: http://genolist.pasteur.fr/SagaList/
Cat  : Organism-specific gene databases
  • SeattleSNPs
Name  : UW-FHCRC Variation Discovery Resource
LinkTp: Implicit; all entries with >= HGNC X-ref and an RT line starting with "SeattleSNPs"
Server: http://pga.gs.washington.edu/
Db_URL: http://pga.gs.washington.edu/data/%s/
Cat  : Polymorphism databases
  • SGD
Name  : Saccharomyces Genome Database
Ref  : Nucleic Acids Res. 35:D468-D471(2007); PubMed:17142221 ; DOI:10.1093/nar/gkl931 ;
LinkTp: Explicit
Server: http://www.yeastgenome.org/
Db_URL: http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=%s
Cat  : Organism-specific gene databases
  • Siena-2DPAGE
Name  : 2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy
LinkTp: Explicit
Server: http://www.bio-mol.unisi.it/2d/2d.html
Cat  : 2D gel databases
  • SMART
Name  : Simple Modular Architecture Research Tool; a protein domain database
Ref  : Nucleic Acids Res. 34:D257-D260(2006); PubMed:16381859 ; DOI:10.1093/nar/gkj079 ;
LinkTp: Explicit
Server: http://smart.embl.de/
Db_URL: http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s
Cat  : Family and domain databases
  • SMR
Name  : SWISS-MODEL Repository - a database of annotated 3D protein structure models
Ref  : Nucleic Acids Res. 34:D315-D318(2006); PubMed:16381875 ; DOI:10.1093/nar/gkj056 ;
LinkTp: Explicit
Server: http://swissmodel.expasy.org/repository/
Db_URL: http://swissmodel.expasy.org/repository/smr.php?sptr_ac=%s
Cat  : 3D structure databases
  • SOURCE
Name  : The Stanford Online Universal Resource for Clones and ESTs
LinkTp: Implicit; All human and mouse entries with >=1 gene name and >= 1 MIM or MGI X-ref.
Server: http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch
Cat  : Other
  • SubtiList
Name  : Bacillus subtilis strain 168 genome database
Ref  : Nucleic Acids Res. 30:62-65(2002); PubMed:11752255 ;
LinkTp: Explicit
Server: http://genolist.pasteur.fr/SubtiList/
Db_URL: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+%s
Cat  : Organism-specific gene databases
  • SWISS-2DPAGE
Name  : Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital
Ref  : Proteomics 4:2352-2356(2004); PubMed:15274128 ; DOI:10.1002/pmic.200300830 ;
LinkTp: Explicit
Server: http://www.expasy.org/ch2d/
Db_URL: http://www.expasy.org/cgi-bin/ch2d-search-ac?%s
Cat  : 2D gel databases
  • TAIR
Name  : The Arabidopsis Information Resource
Ref  : Nucleic Acids Res. 31:224-228(2003); PubMed:12519987 ;
LinkTp: Explicit
Server: http://www.arabidopsis.org/
Db_URL: http://www.arabidopsis.org/servlets/TairObject?type=locus&name=%s
Cat  : Organism-specific gene databases
  • TIGR
Name  : The bacterial database(s) of 'The Institute of Genome Research'
LinkTp: Explicit
Server: http://www.tigr.org/tdb/
Db_URL: http://cmr.tigr.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=%s
Cat  : Genome annotation databases
  • TIGRFAMs
Name  : TIGRFAMs; a protein family database
Ref  : Nucleic Acids Res. 35:D260-D264(2007); PubMed:17151080 ; DOI:10.1093/nar/gkl1043 ;
LinkTp: Explicit
Server: http://www.tigr.org/TIGRFAMs/
Db_URL: http://cmr.tigr.org/tigr-scripts/CMR/HmmReport.cgi?hmm_acc=%s
Cat  : Family and domain databases
  • TRANSFAC
Name  : Transcription factor database
Ref  : Nucleic Acids Res. 34:D108-D110(2006); PubMed:16381825 ; DOI:10.1093/nar/gkj143 ;
LinkTp: Explicit
Server: http://www.gene-regulation.com/
Cat  : Protein family/group databases
  • DNA-binding domain (DBD)
Name  : BDB: Transcription factor prediction database
Ref  : Nucleic Acids Res. 36(Database issue):D88-D92 (2008); DOI:10.1093/nar/gkm964
Server: www.transcriptionfactor.org
  • TubercuList
Name  : Mycobacterium tuberculosis strain H37Rv genome database
LinkTp: Explicit
Server: http://genolist.pasteur.fr/TubercuList/
Cat  : Organism-specific gene databases
  • UniGene
Name  : UniGene gene-oriented nucleotide sequence clusters
Ref  : Nucleic Acids Res. 35:D5-12(2007); PubMed:17170002 ; DOI:10.1093/nar/gkl1031 ;
LinkTp: Explicit
Server: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=UniGene
Db_URL: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s1&CID=%s2
Cat  : Sequence databases
  • UniRef
Name  : UniProt Non-redundant Reference (UniRef) Databases
Ref  : Nucleic Acids Res. 34:D187-D191(2006); PubMed:16381842 ; DOI:10.1093/nar/gkj161 ;
LinkTp: Implicit; all Swiss-Prot and TrEMBL (UniProt knowledgebase) entries
Server: http://www.uniprot.org/database/nref.shtml
Cat  : Other
  • WorfDB
Name  : The C.elegans ORFeome cloning project
Ref  : Nucleic Acids Res. 31:237-240(2003); PubMed:12519990 ;
LinkTp: Implicit; all C.elegans entries with an explicit cross-reference to WormPep
Server: http://worfdb.dfci.harvard.edu/
Db_URL: http://worfdb.dfci.harvard.edu/search.pl?form=1&search=%2
Cat  : Organism-specific gene databases
  • WormBase
Name  : WormBase
Ref  : Nucleic Acids Res. 35:D506-D510(2007); PubMed:17099234 ; DOI:10.1093/nar/gkl818 ;
LinkTp: Explicit
Server: http://www.wormbase.org/
Db_URL: http://www.wormbase.org/db/gene/gene?name=%s
Cat  : Organism-specific gene databases
  • WormPep
Name  : Caenorhabditis elegans genome sequencing project protein database
Ref  : Genomics 46:200-216(1997); PubMed:9417907 ;
LinkTp: Explicit
Server: http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/current/wormpep.shtml
Db_URL: http://www.sanger.ac.uk/cgi-bin/Projects/C_elegans/wormpep_fetch.pl?entry=%s&what=protein&type=exact
Cat  : Organism-specific gene databases
  • Yeast-GFP
Name  : Yeast GFP fusion localization database
Ref  : Nature 425:737-741(2003); PubMed:14562106 ; DOI:10.1038/nature02046 ;
LinkTp: Implicit; All Swiss-Prot entries from Saccharomyces cerevisiae with Y[A-Z]{2}[0-9]{3}[A-Z] in the GN line
Server: http://yeastgfp.ucsf.edu
Db_URL: http://yeastgfp.ucsf.edu/getOrf.php?orf=%s
Cat  : Organism-specific gene databases
  • ZFIN
Name  : Zebrafish Information Network genome database
Ref  : Nucleic Acids Res. 34:D581-D585(2006); PubMed:16381936 ; DOI:10.1093/nar/gkj086 ;
LinkTp: Explicit
Server: http://zfin.org/
Db_URL: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=%s
Cat  : Organism-specific gene databases
  • Aarhus/Ghent-2DPAGE
Name  : Human keratinocyte 2D gel protein database from Aarhus and Ghent universities
Ref  : FEBS Lett. 430:64-72(1998); PubMed:9678596 ;
LinkTp: Explicit
Server: None
Cat  : 2D gel databases
  • ECO2DBASE
Name  : Escherichia coli gene-protein database; a 2-DE gel database
Ref  : Electrophoresis 20:2149-2159(1999); PubMed:9298644 ;
LinkTp: Explicit
Server: None
Note  : Obsolete abbreviation: EC-2D-GEL
Cat  : 2D gel databases
  • StyGene
Name  : Salmonella typhimurium LT2 genome database
LinkTp: Explicit
Server: None
Cat  : Organism-specific gene databases

Other

Note: The following databases will be organised later.

ANISEED AntonosporaDB ATIDB
BeeBase BeetleBase BGD
BioHealthBase Bovine QTL Viewer Cattle EST Gene Family Database
CGD CGL ChromDB
Chromosome 7 Annotation Project CSHLmpd Database of Genomic Variants
DictyBase DroSpeGe EcoCyc
FlyBase Fungal Comparative Genomics Fungal Telomere Browser
Gallus Genome Browser GeneDB GrainGenes
Gramene HapMap Human 2q33
Human Genome Segmental Duplication Database IVDB MAGI
Marine Biological Lab Organism Databases MGI Non-Human Segmental Duplication Database
OMAP OryGenesDB Oryza Chromosome 8
Pathway Tools ParameciumDB PeanutMap
PlantsDB PlasmoDB PseudoCAP
PossumBase PUMAdb RGD
SGD SGD Lite SmedDB
SOL Genomics Network Soybase Soybean Gbrowse Database
T1DBase TAIR TGD
TGI TIGR TIGR Rice Genome Browser
ToxoDB TriAnnot BAC Viewer VectorBase
wFleaBase WormBase
XanthusBase Xenbase

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