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

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.
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https://hal.archives-ouvertes.fr/hal-00194414
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Submitted on : Thursday, December 6, 2007 - 3:15:56 PM
Last modification on : Saturday, July 3, 2021 - 3:40:07 AM

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Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.. Nucleic Acids Research, Oxford University Press, 2007, 35 (Web Server issue), pp.W52-7. ⟨10.1093/nar/gkm360⟩. ⟨hal-00194414⟩

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