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This resource has been developed to allow the comparison of CRISPRs between strains of a given species or between closely related species, and to classify the spacers. It is composed of two main applications.

1- CRISPRcomparison: CRISPRs comparison

When the genome sequence of several strains is available for a given species, and when each strain possesses several CRISPRs, it is important to be able to classify the different CRISPRs, particularly as their position on the genome might vary. A program has been created that automatically recovers from CRISPRdb all members of a genus containing a CRISPR and proposes to compare each of them. Additional strains can be added in the comparison. The comparison is based on the presence of identical DRs and similar flanking sequences (a certain mismatch threshold is accepted).
The result is shown in a table where CRISPRs are grouped. Information is given on their position and on the number of repeats. A link to the corresponding CRISPR in CRISPRdb can be activated.

For example in the genus Yersinia, and at the date of the writing of this tutorial, genome sequence data is available for six Y. pestis and two Y. pseudotuberculosis strains. Four different CRISPRs are found which can each be present in a subset of strains (in this particular case, one of the CRISPR loci is deleted in the leader region of the sequenced Y. pseudotuberculosis strains, and because of this feature is identified as a fourth locus).

When two or more alleles of a given CRISPR are found, the flanking sequences can be aligned and a link is provided to the second application "CRISPRtionary" to annotate and classify the spacers. This can be reached by activating the CompareSpacers button.

2- CRISPRtionary: Spacers Dictionary Creator

This is a very helpful tool to analyse sequences from multiple alleles derived from the same locus. Such data will be produced for instance when investigating the diversity (evolution) of CRISPRs within a species by sequencing the locus in different isolates. This tool can then be used to automatically number spacers, produce a "dictionary", and code the alleles using this dictionary.

Several sequences can be submitted simultaneously in fasta format. CRISPRfinder identifies the consensus DR in each of them and extracts the spacer. In the next page a possibility is given to select the more appropriate DR. It is recommended to select the DR such that from left to right the degenerate DR is first and the leader is last. In this configuration the spacer 1 will be the first after the degenerated DR which corresponds to the oldest spacer inside the CRISPR.

Sample files are provided to illustrate how this works and what it does ( Y. pestis Dictionary and CRISPR_YP1_in Y. pestis).
The following steps need to be followed: