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Nucleic Acids Res. 2007 Jul;35(Web Server issue):W52-7. Epub 2007 May 30.

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

Author information

1
Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, F-91405, France. Ibtissem.Grissa@igmors.u-psud.fr

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.

PMID:
17537822
PMCID:
PMC1933234
DOI:
10.1093/nar/gkm360
[Indexed for MEDLINE]
Free PMC Article

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