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Nucleic Acids Research 2006 34(Web Server issue):W362-W365; doi:10.1093/nar/gkl124
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins

Edouard de Castro1,*, Christian J. A. Sigrist1, Alexandre Gattiker3, Virginie Bulliard1, Petra S. Langendijk-Genevaux1, Elisabeth Gasteiger1, Amos Bairoch1,2 and Nicolas Hulo1

1 Swiss Institute of Bioinformatics (SIB) 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland 2 Structural Biology and Bioinformatics Department, University of Geneva 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland 3 National Institute of Technology and Evaluation 2-49-10 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan

*To whom correspondence should be addressed. Tel: +41 22 379 5050; Fax: +41 22 379 5858; Email: ecastro{at}isb-sib.ch

Received February 14, 2006. Revised March 1, 2006. Accepted March 13, 2006.

ScanProsite—http://www.expasy.org/tools/scanprosite/—is a new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences. For a number of PROSITE profiles, the tool now makes use of ProRules—context-dependent annotation templates—to detect functional and structural intra-domain residues. The detection of those features enhances the power of function prediction based on profiles. Both user-defined sequences and sequences from the UniProt Knowledgebase can be matched against custom patterns, or against PROSITE signatures. To improve response times, matches of sequences from UniProtKB against PROSITE signatures are now retrieved from a pre-computed match database. Several output modes are available including simple text views and a rich mode providing an interactive match and feature viewer with a graphical representation of results.


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