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Nucleic Acids Research Advance Access first published online on May 30, 2007
This version published online on May 31, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm360
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats

Ibtissem Grissa1,*, Gilles Vergnaud1,2 and Christine Pourcel1

1Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, F-91405 and 2Centre d’Etude du Bouchet, 5 rue Lavoisier, 91710 Vert le Petit, France

*To whom correspondence should be addressed. Tel: 33 1 69 15 30 01; Fax: 33 1 69 15 66 78; Email: Ibtissem.Grissa{at}igmors.u-psud.fr

Received January 25, 2007. Revised April 6, 2007. Accepted April 25, 2007.

Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php.


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I. Grissa, G. Vergnaud, and C. Pourcel
CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats
Nucleic Acids Res., April 28, 2008; (2008) gkn228v1.
[Abstract] [Full Text] [PDF]


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