A Guide to UniProt for Protein Scientists

Methods in Molecular Biology

Volumn 694, Issue , 2011, Pages 25-35

  O’Donovan, Claire ^a   Apweiler, Rolf ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

Annotation; Archive; Complete proteome; Nonredundant; Protein sequence database; Stable identifiers

Indexed keywords

PROTEIN; PROTEOME;

ANIMAL; ARTICLE; BIOLOGY; HUMAN; INTERNET; METHODOLOGY; MOLECULAR GENETICS; PROTEIN DATABASE;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; PROTEINS; PROTEOME;

MLCS; MLOWN;

EID: 79951926801     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-977-2_2     Document Type: Chapter

References (13)

1. The UniProt Consortium. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 38, D142–D148.
2. Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R. (2004) UniProt archive. Bioinformatics 20, 3236–3237.
3. Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23, 1282–1288.
4. Kersey P, Hermjakob H, Apweiler R. (2000) VARSPLIC: alternatively-spliced protein sequences derived from Swiss-Prot and TrEMBL. Bioinformatics 16, 1048–1049.
5. Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, Lima T, Kersey P, Pagni M, Sigrist CJ, Lachaize C, et al. (2003) Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem. 27, 49–58.
6. Fleischmann W, Moller S, Gateau A, Apweiler R. (1999) A novel method for automatic functional annotation of proteins. Bioinformatics 15, 228–233.
7. Wu CH, Nikolskaya A, Huang H, Yeh L-S, Natale DA, Vinayaka CR, Hu ZZ, Mazumder R, Kumar S, Kourtesis P, et al. (2004) PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res. 32, D112–D114.
8. Natale DA, Vinayaka CR, Wu CH. (2004) Large-scale, classification-driven, rule-based functional annotation of proteins. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics – Subramaniam S, ed. Bioinformatics John Wiley West Sussex, England.
9. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, et al. (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 36, D1009–D1014.
10. Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, et al. (2008) The Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 36, D577–D581.
11. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al. (2008) Ensembl 2008. Nucleic Acids Res. 36, D707–D714.
12. The Gene Ontology Consortium. (2000) Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29.
13. Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics 4, 1985–1988.