CRISPRFinder: A Web Tool to Identify Clustered Regularly Interspaced Short Palindromic Repeats

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W52-7. doi: 10.1093/nar/gkm360. Epub 2007 May 30.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromosome Mapping / methods*
  • Computational Biology / methods*
  • DNA, Intergenic / genetics*
  • Database Management Systems
  • Databases, Genetic*
  • Genome, Archaeal / genetics*
  • Genome, Bacterial / genetics*
  • Repetitive Sequences, Nucleic Acid / genetics*
  • Software
  • User-Computer Interface*

Substances

  • DNA, Intergenic