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The Universal Protein Resource (UniProt): an expanding universe of protein information
Department of Biochemistry and Molecular Biology, Georgetown University Medical Center 3900 Reservoir Road, NW, Washington, DC 20057-1414, USA 1The EMBL Outstation, The European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK 2Swiss Institute of Bioinformatics, Centre Medical Universitaire 1 rue Michel Servet, 1211 Geneva 4, Switzerland 3National Biomedical Research Foundation 3900 Reservoir Road, NW, Washington, DC 20057-1414, USA
*To whom correspondence should be addressed. Tel: +44 1223 494435; Fax: +44 1223 494468; Email: apweiler{at}ebi.ac.uk
Received September 17, 2005. Revised October 31, 2005. Accepted October 31, 2005.
The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/.
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