Abstract
The Universal Protein Resource (UniProt, http://www.uniprot.org) consortium is an initiative of the SIB Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) to provide the scientific community with a central resource for protein sequences and functional information. The UniProt consortium maintains the UniProt KnowledgeBase (UniProtKB), updated every 4 weeks, and several supplementary databases including the UniProt Reference Clusters (UniRef) and the UniProt Archive (UniParc).
The Swiss-Prot section of the UniProt KnowledgeBase (UniProtKB/Swiss-Prot) contains publicly available expertly manually annotated protein sequences obtained from a broad spectrum of organisms. Plant protein entries are produced in the frame of the Plant Proteome Annotation Program (PPAP), with an emphasis on characterized proteins of Arabidopsis thaliana and Oryza sativa. High level annotations provided by UniProtKB/Swiss-Prot are widely used to predict annotation of newly available proteins through automatic pipelines.
The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry. We will also present some of the tools and databases that are linked to each entry.
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Acknowledgments
UniProt is mainly supported by the National Institutes of Health (NIH) grant 1 U41 HG006104. Additional support for the EBI’s involvement in UniProt comes from the NIH grant 2P41 HG02273. Swiss-Prot activities at the SIB are supported by the Swiss Federal Government through The State Secretariat for Education, Research and Innovation SERI. PIR’s UniProt activities are also supported by the NIH grants 5R01GM080646-07, 3R01GM080646-07S1, 5G08LM010720-03, and 8P20GM103446-12, and the National Science Foundation (NSF) grant DBI-1062520. We would like to thank all Swiss-Prot curators and developers for their contribution to the expert annotation of proteins and their critical reading of the manuscript.
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Boutet, E. et al. (2016). UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 1374. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3167-5_2
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DOI: https://doi.org/10.1007/978-1-4939-3167-5_2
Publisher Name: Humana Press, New York, NY
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Online ISBN: 978-1-4939-3167-5
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