How to identify CRISPRs in sequencing data.

Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences composed of a succession of repeats (23-50 bp long) separated by unique sequences called spacers. CRISPRs together with a set of genes called cas for CRISPR associated, constitute a defence mechanism against invasion by foreign sequences. We describe protocols and bioinformatics tools that allow the identification of CRISPRs, their comparison and their component determination (the direct repeats and the spacers). A schematic representation of the spacer organization can be produced, allowing an easy comparison between strains.