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Swiss-Prot is a manually curated biological database of protein sequences.[1][2] Swiss-Prot was created in 1986 by Amos Bairoch during his PhD and developed by the Swiss Institute of Bioinformatics and the European Bioinformatics Institute.[3][4] Swiss-Prot strives to provide reliable protein sequences associated with a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.

Contents

UniProt consortium

In 2002, the UniProt consortium was created:[5][6] it is a collaboration between the Swiss Institute of Bioinformatics, the European Bioinformatics Institute and the Protein Information Resource (PIR), funded by the National Institutes of Health. Swiss-Prot and its automatically curated supplement TrEMBL, have joined with the Protein Information Resource protein database to produce the UniProt Knowledgebase, the world's most comprehensive catalogue of information on proteins.[7]

The UniProt consortium produced 3 database components, each optimised for different uses. The UniProt Knowledgebase (UniProtKB [Swiss-Prot + TrEMBL]), the UniProt Non-redundant Reference (UniRef) databases,[8] which combine closely related sequences into a single record to speed similarity searches and the UniProt Archive (UniParc),[9] which is a comprehensive repository of protein sequences, reflecting the history of all protein sequences.

Statistics

UniProt Knowledgebase Release 15.5 consists of:

  • UniProtKB/Swiss-Prot Release 57.5 (07-Jul-2009): 470,369 entries
  • UniProtKB/TrEMBL Release 40.5 (07-Jul-2009): 8,594,382 entries

References

  1. ^ Boeckmann B, Bairoch A, Apweiler R, et al. (January 2003). "The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003". Nucleic Acids Res. 31 (1): 365–70. doi:10.1093/nar/gkg095. PMID 12520024. PMC 165542. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=12520024. 
  2. ^ Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A (2007). "UniProtKB/Swiss-Prot". Methods Mol. Biol. 406: 89–112. doi:10.1007/978-1-59745-535-0_4. PMID 18287689. 
  3. ^ Bairoch Amos (2000). "Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!". Bioinformatics 16: 48–64. doi:10.1093/bioinformatics/16.1.48. PMID 10812477.  — a historical account by Bairoch.
  4. ^ Séverine Altairac, "Naissance d’une banque de données: Interview du prof. Amos Bairoch". Protéines à la Une, August 2006. ISSN 1660-9824.
  5. ^ Bairoch A, Apweiler R, Wu CH, et al. (January 2005). "The Universal Protein Resource (UniProt)". Nucleic Acids Res. 33 (Database issue): D154–9. doi:10.1093/nar/gki070. PMID 15608167. PMC 540024. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15608167. 
  6. ^ "The Universal Protein Resource (UniProt) 2009". Nucleic Acids Res. 37: D169. October 2008. doi:10.1093/nar/gkn664. PMID 18836194. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=18836194. 
  7. ^ Wu CH, Apweiler R, Bairoch A, et al. (January 2006). "The Universal Protein Resource (UniProt): an expanding universe of protein information". Nucleic Acids Res. 34 (Database issue): D187–91. doi:10.1093/nar/gkj161. PMID 16381842. 
  8. ^ Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH (May 2007). "UniRef: comprehensive and non-redundant UniProt reference clusters". Bioinformatics 23 (10): 1282–8. doi:10.1093/bioinformatics/btm098. PMID 17379688. http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=17379688. 
  9. ^ Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R (November 2004). "UniProt archive". Bioinformatics 20 (17): 3236–7. doi:10.1093/bioinformatics/bth191. PMID 15044231. http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15044231. 

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