The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Journal: 2003/March - Nucleic Acids Research
ISSN: 1362-4962
PUBMED: 12520024
Abstract:
The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org.
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Nucleic Acids Res 31(1): 365-370

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

+3 authors
Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland The EMBL Outstation—The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
To whom correspondence should be addressed. Email: hc.bis-bsi@nnamkceob.ettigirb
Received 2002 Sep 16; Revised 2002 Oct 23; Accepted 2002 Oct 23.

Abstract

The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at gro.ysapxe@torp-ssiws.

Abstract

ACKNOWLEDGEMENTS

We wish to thank Andrea Auchincloss, Livia Famiglietti and Michele Magrane for helpful discussions, and Vivienne Baillie Gerritsen for the correction of the manuscript. All statistical information given in this article is retrieved from SWISS-PROT release 40.27 (August 2002) and TrEMBL release 21.10 (September 2002), respectively.

ACKNOWLEDGEMENTS

REFERENCES

REFERENCES

References

  • 1. O'Donovan C., Martin,M.J., Gattiker,A., Gasteiger,E., Bairoch,A. and Apweiler,R. (2002) High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief. Bioinform., 3, 275–284. [[PubMed]
  • 2. Stoesser G., Baker,W., van den Broek,A., Camon,E., Garcia-Pastor,M., Kanz,C., Kulikova,T., Leinonen,R., Lin,Q., Lombard,V. et al. (2002) The EMBL Nucleotide Sequence Database. Nucleic Acids Res., 30, 21–26.
  • 3. Kersey P., Hermjakob,H. and Apweiler,R. (2000) VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL. Bioinformatics, 11, 1048–1049. [[PubMed]
  • 4. O'Donovan C., Martin,M.J., Glemet,E., Codani,J.-J. and Apweiler,R. (1999) Removing redundancy in SWISS-PROT and TrEMBL. Bioinformatics, 15, 258–259. [[PubMed]
  • 5. Apweiler R(2001) Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences. Brief. Bioinform., 2, 9–18. [[PubMed][Google Scholar]
  • 6. O'Donovan C., Apweiler,R. and Bairoch,A. (2001) The human proteomics initiative (HPI). Trends Biotechnol., 19, 178–181. [[PubMed]
  • 7. Brett D., Pospisil,H., Valcarcel,J., Reich,J. and Bork,P. (2002) Alternative splicing and genome complexity. Nature Genet., 30, 29–30. [[PubMed]
  • 8. Modrek B. and Lee,C. (2002) A genomic view of alternative splicing. Nature Genet., 1, 13–19. [[PubMed]
  • 9. Wheeler D.L., Church,D.M., Lash,A.E., Leipe,D.D., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Tatusova,T.A., Wagner,L. and Rapp,B.A. (2002) Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res., 30, 13–16.
  • 10. Rebhan M., Chalifa-Caspi,V., Prilusky,J. and Lancet,D. (1998) GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics, 14, 656–664. [[PubMed]
  • 11. Lenhard B., Hayes,W.S. and Wasserman,W.W. (2001) GeneLynx: a gene-centric portal to the human genome. Genome Res., 11, 2151–2157.
  • 12. Wain H.M., Lush,M., Ducluzeau,F. and Povey,S. (2002) Genew: the human gene nomenclature database. Nucleic Acids Res., 30, 169–171.
  • 13. Deloukas P., Matthews,L.H., Ashurst,J., Burton,J., Gilbert,J.G., Jones,M., Stavrides,G., Almeida,J.P., Babbage,A.K., Bagguley,C.L. et al. (2001) The DNA sequence and comparative analysis of human chromosome 20. Nature, 414, 865–871. [[PubMed]
  • 14. Hattori M., Fujiyama,A., Taylor,T.D., Watanabe,H., Yada,T., Park,H.S., Toyoda,A., Ishii,K., Totoki,Y., Choi,D.K. et al. (2000) The DNA sequence of human chromosome 21. Nature, 405, 311–319. [[PubMed]
  • 15. Dunham I., Shimizu,N., Roe,B.A., Chissoe,S., Hunt,A.R., Collins,J.E., Bruskiewich,R., Beare,D.M., Clamp,M., Smink,L.J. et al. (1999) The DNA sequence of human chromosome 22. Nature, 402, 489–495. [[PubMed]
  • 16. Ashburner M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet., 25, 25–29.
  • 17. Pruitt K.D. and Maglott,D.R. (2001) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res., 29, 137–140.
  • 18. Apweiler R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Cerutti,L., Corpet,F., Croning,M.D. et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37–40.
  • 19. Fleischmann R.D., Adams,M.D., White,O., Clayton,R.A., Kirkness,E.F., Kerlavage,A.R., Bult,C.J., Tomb,J.-F., Dougherty,B.A., Merrick,J.M. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496–512. [[PubMed]
  • 20. Gasteiger E., Jung,E. and Bairoch,A. (2001) SWISS-PROT: connecting biomolecular knowledge via a protein database. Curr. Issues Mol. Biol., 3, 47–55. [[PubMed]
  • 21. Cooper C.A., Harrison,M.J., Wilkins,M.R. and Packer,N.H. (2001) GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources. Nucleic Acids Res., 29, 332–335.
  • 22. Fleischmann W., Moeller,S., Gateau,A. and Apweiler,R. (1999) A novel method for automatic and reliable functional annotation. Bioinformatics, 15, 228–233. [[PubMed]
  • 23. Falquet L., Pagni,M., Bucher,P., Hulo,N., Sigrist,C.J.A., Hofmann,K. and Bairoch,A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res., 30, 235–238.
  • 24. Attwood T.K., Blythe,M.J., Flower,D.R., Gaulton,A., Mabey,J.E., Maudling,N., McGregor,L., Mitchell,A.L., Moulton,G., Paine,K. and Scordis,P. (2002) PRINTS and PRINTS-S shed light on protein ancestry. Nucleic Acids Res., 30, 239–241.
  • 25. Bateman A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L.L. (2002) The Pfam Protein Families Database. Nucleic Acids Res., 30, 276–280.
  • 26. Corpet F., Servant,F., Gouzy,J. and Kahn,D. (2000) ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res., 28, 267–269.
  • 27. Letunic I., Goodstadt,L., Dickens,N.J., Doerks,T., Schultz,J., Mott,R., Ciccarelli,F., Copley,R.R., Ponting,C.P. and Bork,P. (2002) Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res., 30, 242–244.
  • 28. Haft D.H., Loftus,B.J., Richardson,D.L., Yang,F., Eisen,J.A., Paulsen,I.T. and White,O. (2001) TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res., 29, 41–43.
  • 29. Etzold T. and Argos,P. (1993) SRS—an indexing and retrieval tool for flat file data libraries. Comput. Appl. Biosci., 9, 49–57. [[PubMed]
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