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Groups - Geneva - Swiss-Prot - I. Xenarios
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Summary

The Swiss-Prot group develops, annotates and maintains the UniProtKB/Swiss-Prot protein sequence database, the most widely used protein information resource in the world. The group also develops and maintains other databases including PROSITE, a database of protein families and domains, and ENZYME, a database of enzyme nomenclature. The group also co-heads the development and maintenance of the ExPASy proteomics website.
The Swiss-Prot group is by far the largest group in the Swiss Institute of Bioinformatics.
 

Introduction

It has recently become obvious that studying only gene (DNA) sequences is insufficient to give a complete description of the proteins they encode. Furthermore DNA provides little informa­tion about protein function, their post-translation modifications, other proteins they interact with, or their location in cells and organisms. As the sequencing of many genomes nears completion, scientists are focusing their research efforts on the proteins they encode.
 

Projects and Services

UniProtKB/Swiss-Prot

The Swiss-Prot group develops and maintains the UniProtKB/Swiss-Prot database. This task is performed in collaboration with the European Bioinformatics Institute (EBI) in Hinxton (UK) and the Protein Information Resource (PIR) in Georgetown (USA). These three groups form together the Universal Protein Resource (UniProt) consortium whose mission is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. This collaborative effort is mainly funded by the Swiss Confederation, the NIH, the EMBL and the European Union.
Swiss-Prot provides concise, but thorough, descriptions of a non-redundant set of proteins including their function, domain structure, post-translational modifications and variants. Swiss-Prot is tightly integrated with other databases. Its high-quality annotation is the fruit of manual curation by expert biologists, who use information available in the scientific literature to provide an accurate description of each protein’s features. Swiss-Prot concentrates on model organisms of distinct taxonomic groups to ensure the presence of high-quality annotation for representative members of all protein families. Special attention is paid to the annotation of proteins from human and other mammals (HPI program), bacteria and archaea (HAMAP), plants (PPAP), fungi (FPAP), viruses, Drosophila, Xenopus, Zebrafish, C. elegans, as well as animal toxins (Tox-Prot).
While manual annotation is a task that can be streamlined, it cannot cope with the speed at which new sequence data are accumulating. To address this challenge, the Swiss-Prot group is developing complex software tools that allow part of the sequence data to be automatically and accurately annotated. New tools are being elaborated to predict post-translational modi­fications and literature data-mining metho­dologies are under development.
 

PROSITE & ENZYME

The Swiss-Prot group develops and maintains other databases, including PROSITE, a database of pro­tein families and domains, and ENZYME, a database of enzyme nomenclature.

 

ExPASy

The ExPASy website, set up in 1993, was the first Internet portal in the life sciences. The portal is an entry point to several databases, including those developed by the different SIB groups and to various online bioinformatics tools. The Swiss-Prot group participates in maintaining and further developing the ExPASy websites together with the SIB Web Team.

 

Publications

Swiss-Prot expertise in the field of protein biology serves the public at large and the scientific community. The group produces Protein Spotlight, a periodic review on proteins, and maintains a server Protéines à la Une providing basic information on the world of proteins in French.
 

Websites for Further Information

Swiss-Prot Group web.expasy.org/groups/swissprot/

ExPASy http://www.expasy.org/

UniProtKB/Swiss-Prot http://web.expasy.org/docs/swiss-prot_guideline.html

Protein Spotlight http://web.expasy.org/spotlight/

Protéines à la Une http://web.expasy.org/prolune/

 

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