Difference between revisions of "Bioinformatics databases links"

Revision as of 02:55, 30 June 2008 (view source) Christoph (Talk | contribs) (→‎Other) ← Older edit		Revision as of 04:56, 12 July 2008 (view source) Christoph (Talk | contribs) (→‎Misc) Newer edit →
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	===Misc===		===Misc===
	*[http://genomics.senescence.info/species/query.php?show=5&sort=4&page=1 AnAge Database] — lists the average lifespans of many species.		*[http://genomics.senescence.info/species/query.php?show=5&sort=4&page=1 AnAge Database] — lists the average lifespans of many species.
		+	*[http://www.genenames.org/data/gdlw_index.html GeneNames: Database Downloads] — for the human genome
	[[Category:Bioinformatics| ]]		[[Category:Bioinformatics| ]]

---

Revision as of 04:56, 12 July 2008

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

Misc

• AnAge Database — lists the average lifespans of many species.
• GeneNames: Database Downloads — for the human genome