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

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

Free PMC article

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

Ibtissem Grissa et al. Nucleic Acids Res. .
Free PMC article


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


Figure 1.
Figure 1.
CRISPR Finder flow chart. (Step 1) Browsing the maximal repeats to get possible CRISPR localizations using the Vmatch program. (Step 2) Consensus DR selection according to candidate occurrences and a score computation: the score privileges internal mismatches between direct repeats of a cluster rather than boundary mismatches. (Step 3) DR and spacers size check. (Step 4) Tandem repeats elimination using ClustalW for aligning spacers.
Figure 2
Figure 2
An example of CRISPRFinder output using the Aquifex aeolicus VF5 genomic sequence (Refseq: NC_000918). (Panel A) (1) Home page where the genomic sequence is submitted. (2) Table listing the detected CRISPRs candidates (questionable and confirmed) providing links to each one. (3) CRISPRs details, the DR is showed in yellow and the spacers in different colours. (4) A fasta file displaying the first CRISPR spacers. (5) Figure showing the Aquifex circular chromosome with CRISPRs positions. (Panel B) One or several spacers may be blasted against NCBI databases by clicking on the blast_spacers button. (Panel C) The flanking and the CRISPR sequences may be viewed by clicking on the Get sequences button. The sequences boundaries may be modified by the user. (Panel D) The list of consensus DRs for all CRISPRs is shown with a link to identical DRs in the CRISPR database.

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