Skip Navigation



Nucleic Acids Research Advance Access published online on October 25, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp885
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (3153K) Freely available
Right arrow Screen PDF (555K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Sigrist, C. J. A.
Right arrow Articles by Hulo, N.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sigrist, C. J. A.
Right arrow Articles by Hulo, N.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

PROSITE, a protein domain database for functional characterization and annotation

Christian J. A. Sigrist1,*, Lorenzo Cerutti1, Edouard de Castro1, Petra S. Langendijk-Genevaux1, Virginie Bulliard1, Amos Bairoch1,2 and Nicolas Hulo1

1Swiss Institute of Bioinformatics (SIB), Centre Médical Universitaire and 2Structural Biology and Bioinformatics Department, University of Geneva, 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland

*To whom correspondence should be addressed. Tel: +41 22 379 58 68; Fax: +41 22 379 58 58; Email: christian.sigrist{at}isb-sib.ch

Received September 3, 2009. Revised October 2, 2009. Accepted October 2, 2009.

PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE is largely used for the annotation of domain features of UniProtKB/Swiss-Prot entries. Among the 983 (DNA-binding) domains, repeats and zinc fingers present in Swiss-Prot (release 57.8 of 22 September 2009), 696 (~70%) are annotated with PROSITE descriptors using information from ProRule. In order to allow better functional characterization of domains, PROSITE developments focus on subfamily specific profiles and a new profile building method giving more weight to functionally important residues. Here, we describe AMSA, an annotated multiple sequence alignment format used to build a new generation of generalized profiles, the migration of ScanProsite to Vital-IT, a cluster of 633 CPUs, and the adoption of the Distributed Annotation System (DAS) to facilitate PROSITE data integration and interchange with other sources. The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.