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. 2008 Jul 1;36(Web Server issue):W145-8.
doi: 10.1093/nar/gkn228. Epub 2008 Apr 28.

CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats

Ibtissem Grissa  1 , Gilles Vergnaud, Christine Pourcel
Affiliations

CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats

Ibtissem Grissa et al. Nucleic Acids Res. .

Abstract

Clustered regularly interspaced short palindromic repeat (CRISPR) elements are a particular family of tandem repeats present in prokaryotic genomes, in almost all archaea and in about half of bacteria, and which participate in a mechanism of acquired resistance against phages. They consist in a succession of direct repeats (DR) of 24-47 bp separated by similar sized unique sequences (spacers). In the large majority of cases, the direct repeats are highly conserved, while the number and nature of the spacers are often quite diverse, even among strains of a same species. Furthermore, the acquisition of new units (DR + spacer) was shown to happen almost exclusively on one side of the locus. Therefore, the CRISPR presents an interesting genetic marker for comparative and evolutionary analysis of closely related bacterial strains. CRISPRcompar is a web service created to assist biologists in the CRISPR typing process. Two tools facilitates the in silico investigation: CRISPRcomparison and CRISPRtionary. This website is freely accessible at http://crispr.u-psud.fr/CRISPRcompar/.

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Figures

Figure 1.
Figure 1.
Example of CRISPRcompar and CRISPRtionary output using the three S. thermophilus genomic sequences (RefSeq: NC_006449, NC_008532, NC_006448). (A) Table showing the classification of the different CRISPRs. Three CRISPRs are identified, of which two are found in two or more strains. (B) CRISPR_2 sequences are submitted to the CRISPRtionary program. (C) The spacers are labelled and different files can be recovered.
Figure 2.
Figure 2.
Schematic representation of the CRISPR repeats organization in four M. tuberculosis and two M. bovis strains. The binary file produced by CRISPRtionary, after the spacers have been re-annotated, is used to produce a figure in which the presence of a spacer is indicated by a dark square. The detail of the spacer composition for each strain is indicated in the bottom part of the figure.
See this image and copyright information in PMC

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