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Bioinformatics Advance Access published online on October 21, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp586
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© 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.

CRISPI: a CRISPR Interactive database

Christine Rousseau 1,*, Jacques Nicolas 1,* and Mathieu Gonnet 2

1IRISA-INRIA, Campus de Beaulieu, 35042 Rennes cedex, France
2UMR 6197 Microbiologie des environnements extrêmes, technopôle Brest-Iroise, BP 70 29280Plouzané, France.

*To whom correspondence should be addressed. Miss Christine Rousseau, E-mail: croussea{at}irisa.fr, jnicolas{at}irisa.fr


  Abstract

Summary: The CRISPR genomic structures (Clustered Regularly Interspaced Short Palindromic Repeats) form a family of repeats that is largely present in archaea and frequent in bacteria. On the basis of a formal model of CRISPR using very few parameters, a systematic study of all their occurrences in all available genomes of Archaea and Bacteria has been carried out. This has resulted in a relational database, CRISPI, which also includes a complete repertory of associated CRISPR-associated genes (CAS). A userfriendly web interface with many graphical tools and functions allows users to extract results, find CRISPR in personal sequences or calculate sequence similarity with spacers.

Availability: CRISPI free access at http://crispi.genouest.org

Contact: jnicolas{at}irisa.fr

Associate Editor: Prof. Dmitrij Frishman

Received on May 29, 2009; revised on October 6, 2009; accepted on October 7, 2009

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