CRISPRDetect help

(last update of help was on 1/3/2021 by CMB)

17 7 2019. CRISPRDetect version 2.4 (download)

Version 2.4 has some bug fixes (compared to 2.2) , update to the CRISPRDirection (v2) module, and extends the CRISPR I-E identification of repeats. The array score is nowalso in the gff3 file. The gff3 file and txt files can be downloaded directly from the web output. The web interface uses a similar version with additions for the web inferface.

7 5 2018. Updated CRISPRDirection module with an increase in accuracy for Type II direction calls. Modified to handle gbff files (e.g. GCF or GCA) and cas gene annotations in these.

6 5 2016. CRISPRDetect is a tool to discover and explore the CRISPR non coding RNAs in sequence data. It is a bioinformatic tool to find CRISPR arrays. It is part of CRISPRSuite. The final submission version of CRISPRDetect v2.2 is described and available here. All earlier released presubmision '1' or 2.0 versions were testing versions and may have minor bugs.

News about CRISPRSuite is here:

For enquiries contact chris.brown at

10/8/2016 v2.2 Minor fixes. Changed gff3 output to prevent warning messages on gff3 validation (e.g. Artemis). As spacer is not\ valid in the GO ontology used 'binding_site' instead as a label- the spacer is a nucleic acid binding site.
1/6/2016 v2.1 The final submission version of CRISPRDetect v2.1 is described and available here. All earlier released presubmision '1' or 2.0 versions were testing versions and may have minor bugs, please update to 2.1 or later.


CRISPRDetect is part of CRISPRSuite (more information)
For enquiries contact
  • If you use CRISPRDetect please cite:
    Biswas, A., Staals, R.J. Morales, S.E. Fineran, P.C., and Brown,C.M. (2016) CRISPRDetect: A flexible algorithm to define CRISPR arrays BMC Genomics 17:365 link  

   Input section:

1. Input sequence and parameters

2. Search putative CRISPRs using the following options

3. Filter out poor CRISPRs using one or more of the following parameters

4. Optional parameters [can be modified once the output is generated]

Output Section

Re-running selected modules and other usefule options

Predicted array:



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36.	Yosef, I., M.G. Goren and U. Qimron, (2012) Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res, 40:5569-76.
37.	Vercoe, R.B., J.T. Chang, R.L. Dy, C. Taylor, T. Gristwood, J.S. Clulow, C. Richter, R. Przybilski, A.R. Pitman and P.C. Fineran, (2013) Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands. PLoS Genet, 9:e1003454.
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