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Bioinformatics Advance Access originally published online on August 9, 2005
Bioinformatics 2005 21(21):4060-4066; doi:10.1093/bioinformatics/bti614
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

ProRule: a new database containing functional and structural information on PROSITE profiles

Christian J. A. Sigrist *, Edouard De Castro , Petra S. Langendijk-Genevaux , Virginie Le Saux , Amos Bairoch 1 and Nicolas Hulo

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

*To whom correspondence should be addressed.

Motivation: Increase the discriminatory power of PROSITE profiles to facilitate function determination and provide biologically relevant information about domains detected by profiles for the annotation of proteins.

Summary: We have created a new database, ProRule, which contains additional information about PROSITE profiles. ProRule contains notably the position of structurally and/or functionally critical amino acids, as well as the condition they must fulfill to play their biological role. These supplementary data should help function determination and annotation of the UniProt Swiss-Prot knowledgebase. ProRule also contains information about the domain detected by the profile in the Swiss-Prot line format. Hence, ProRule can be used to make Swiss-Prot annotation more homogeneous and consistent. The format of ProRule can be extended to provide information about combination of domains.

Availability: ProRule can be accessed through ScanProsite at http://www.expasy.org/tools/scanprosite. A file containing the rules will be made available under the PROSITE copyright conditions on our ftp site (ftp://www.expasy.org/databases/prosite/) by the next PROSITE release.

Contact: christian.sigrist{at}isb-sib.ch

Received on May 18, 2005; revised on July 8, 2005; accepted on August 3, 2005

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