CRISPRs Web service User's manual


Site description

Data summary

A number of tools are available here:

CRISPRdb Navigation

The first database page displays the list of prokaryotic public genomes (stored in the database and updated frequently). The species may be displayed in two ways :

The colour code indicates whether a CRISPR has been detected or not: strains without a CRISPR are coloured in yellow, strains having at least one CRISPR are coloured in pink and strains having only questionable CRISPRs are in orange.

Upon selecting a strain name, a page displays the strain properties, the available genomes (chromosome and plasmids) and indicates how many CRISPRs have been found. The colour code is the same as above.
The button leads to the CRISPRs properties page giving more details on the found CRISPRs. The button Find cas genes leads to a table showing the list of CRISPR-associated genes annotated in all the genomes (plasmids or chromosomes) in the corresponding taxon and their position on the genome.

The CRISPRs properties page, indicates the CRISPR's id together with its position on the genome, the number of spacers and the consensus DR sequence.

Querying a CRISPR locus leads to a page containing all its properties : the DR consensus shown in yellow, the spacers shown in different colours, their positions in the genome.

CRISPR Utilities

This page provides a global overview of CRISPRs present in the database and offers the possibility of downloading some overview files.


The BLAST against the CRISPRdb database finds regions of local similarity between the introduced nucleotide sequence(s) and the catalogue of DRs or (and) spacers of confirmed CRISPRs.
It is used as follows:




The Spacer Dictionnary Creator use is illustrated by an example based on Yersinia pestis sample data (see related paper ).
The user should introduce: Next, the user has to select the sheet (of the excel dicitonnary to be used in the analysis.
Then, each sequence of the fasta file will be analyzed by CRISPRFinder and the related CRISPR will be detected. In some cases, no CRISPR is detected because the Direct Repeat sequences are too diverged but this problem will be treated in the next step.
As the sequences are generally short or may contain some sequencing errors, the DR of each cluster may be not defined accurately in this step, so the user should select manually one DR among the obtained DRs listed as shown by the following figure. When identical DRs are detected in the database, a link for more details on it appears next to the DR sequence. This may help the user in selecting the appropriate DR sequence.

Finally, the selected DR will be blasted against all the introduced sequences and all the CRISPRs will be shown (even degenerated ones that did not appear in the previous page). An id will be assigned to each spacer. The id is either selected from the dictionnary (when the spacer is already in the dictionnary) or assigned a number and added to the dictionnary (if it is not listed in the dictionnary).

Colour code

The colour code indicates whether a CRISPR has been detected or not:

Species without a CRISPR are coloured in yellow, species having at least one CRISPR are coloured in pink and species having only questionable CRISPRs are in orange.

Questionable CRISPRs

There are two kinds of "questionable" CRISPRs:

They stop being questionable if the DR consensus is found elsewhere in the database in a convincing CRISPR.
Many of these structures are not true CRISPRs, and they need to be critically investigated. One way to "critically investigate" is to see if the questionable CRISPR seems to be within a coding sequence. CRISPR are usually non-coding, and do not belong to genes. An other way is to check the internal conservation of the candidate DRs, and the divergence of the candidate spacers. More definitive evidence might be provided by the typing of a collection of strains from this species. Some bench work is needed there.

Useful links