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Oxford University Press, Nucleic Acids Research, Web Server(35), p. W52-W57, 2007

DOI: 10.1093/nar/gkm360

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

Journal article published in 2007 by Ibtissem Grissa, Gilles Vergnaud ORCID, Christine Pourcel ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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.