UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View

  • Emmanuel Boutet
  • Damien Lieberherr
  • Michael Tognolli
  • Michel Schneider
  • Parit Bansal
  • Alan J. Bridge
  • Sylvain Poux
  • Lydie Bougueleret
  • Ioannis Xenarios
Part of the Methods in Molecular Biology book series (MIMB, volume 1374)

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.

Key words

Swiss-Prot TrEMBL UniProt Protein database Amino-acid sequence Manual annotation 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Emmanuel Boutet
    • 1
  • Damien Lieberherr
    • 1
  • Michael Tognolli
    • 1
  • Michel Schneider
    • 1
  • Parit Bansal
    • 1
  • Alan J. Bridge
    • 1
  • Sylvain Poux
    • 1
  • Lydie Bougueleret
    • 1
  • Ioannis Xenarios
    • 1
    • 2
  1. 1.Swiss Institute of BioinformaticsCentre Medical UniversitaireGeneva 4Switzerland
  2. 2.University of LausanneLausanneSwitzerland

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