Springer Protocols: Abstract: UniProtKB/Swiss-Prot: The Manually Annotated Section of the UniProt KnowledgeBase

UniProtKB/Swiss-Prot: The Manually Annotated Section of the UniProt KnowledgeBase

By: Emmanuel Boutet², Damien Lieberherr², Michael Tognolli², Michel Schneider², Amos Bairoch²

Abstract

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The Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI), and the Protein Information Resource (PIR) form the Universal Protein Resource (UniProt) consortium. Its main goal is to provide the scientific community with a central resource for protein sequences and functional information. The UniProt consortium maintains the UniProt KnowledgeBase (UniProtKB) and several supplementary databases including the UniProt Reference Clusters (UniRef) and the UniProt Archive (UniParc). (1) UniProtKB is a comprehensive protein sequence knowledgebase that consists of two sections: UniProtKB/Swiss-Prot, which contains manually annotated entries, and UniProtKB/TrEMBL, which contains computer-annotated entries. UniProtKB/Swiss-Prot entries contain information curated by biologists and provide users with cross-links to about 100 external databases and with access to additional information or tools. (2) The UniRef databases (UniRef100, UniRef90, and UniRef50) define clusters of protein sequences that share 100, 90, or 50% identity. (3) The UniParc database stores and maps all publicly available protein sequence data, including obsolete data excluded from UniProtKB. The UniProt databases can be accessed online (http://www.uniprot.org/) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every 2 weeks. The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry, paying particular attention to the specificities of plant protein annotation. We will also present some of the tools and databases that are linked to each entry.

Affiliation(s): (2) Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland

Book Title: Plant Bioinformatics: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 406 | Pub. Date: Dec-01-2007 | Page Range: 89-112 | DOI: 10.1007/978-1-59745-535-0_4

Subject: Plant Sciences

Key Words: Swiss-Prot - TrEMBL - UniProt - protein database - amino-acid sequence - manual annotation

References

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