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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

Ibtissem Grissa  1 , Gilles Vergnaud, Christine Pourcel
Affiliations

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

Ibtissem Grissa et al. Nucleic Acids Res. 2007 Jul.

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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Figures

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.
See this image and copyright information in PMC

References

    1. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J. Bacteriol. 1987;169:5429–5433. - PMC - PubMed
    1. Mojica FJ, Ferrer C, Juez G, Rodriguez-Valera F. Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol. Microbiol. 1995;17:85–93. - PubMed
    1. Mojica FJ, Diez-Villasenor C, Soria E, Juez G. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol. Microbiol. 2000;36:244–246. - PubMed
    1. Peng X, Brugger K, Shen B, Chen L, She Q, Garrett RA. Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes. J. Bacteriol. 2003;185:2410–2417. - PMC - PubMed
    1. van Embden JD, van Gorkom T, Kremer K, Jansen R, van Der Zeijst BA, Schouls LM. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. J. Bacteriol. 2000;182:2393–2401. - PMC - PubMed

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