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

TLDR

CRISPRs are tandem repeats found in many prokaryotic genomes, composed of conserved direct repeats and unique spacers, flanked by a leader sequence that may act as a promoter and are thought to form an RNA‑interference‑based immune system. The authors present CRISPRFinder, a web service that detects CRISPRs, defines direct repeats and spacers, retrieves flanking leader sequences, BLASTs spacers against GenBank, and checks repeat occurrences in other prokaryotic genomes. CRISPRFinder is freely available at http://crispr.u-psud.fr/Server/CRISPRfinder.php.

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.