CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.
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.
Grissa
Ibtissem
I
Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, F-91405, France. Ibtissem.Grissa@igmors.u-psud.fr
Vergnaud
Gilles
G
Pourcel
Christine
C
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D021901:DNA, Intergenic / Q000235:genetics*; D003628:Database Management Systems; D030541:Databases, Genetic; D020745:Genome, Archaeal / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012984:Software; D014584:User-Computer Interface
D021901:DNA, Intergenic