CRISPR pp 77-89 | Cite as

Computational Detection of CRISPR/crRNA Targets

  • Ambarish Biswas
  • Peter C. Fineran
  • Chris M. BrownEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1311)


The CRISPR-Cas systems in bacteria and archaea provide protection by targeting foreign nucleic acids. The sequence of the “spacers” within CRISPR arrays specifically determines the targets in invader genomes. These spacers provide the short specific RNA nucleotide sequences within the guide crRNAs. In addition to complementarity in the spacer–target (protospacer) interaction, short flanking protospacer adjacent motifs (PAMs), or mismatching flanks have a discriminatory role in accurate target detection. Here, we describe a bioinformatic method, called CRISPRTarget, to use the sequence of a CRISPR array (e.g., predicted via CRISPRDetect/CRISPRDirection) to identify the foreign nucleic acids it targets.

Key words

CRISPR-Cas RNAi Protospacer adjacent motifs crRNA Noncoding RNA 



This work was supported by a Rutherford Discovery Fellowship from the Royal Society of NZ to PCF, by a Human Frontier Science Program Grant to Ian Macara, Anne Spang and CMB. AB was a recipient of a University of Otago Postgraduate Scholarship and a Postgraduate Publishing Bursary.


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Ambarish Biswas
    • 1
  • Peter C. Fineran
    • 2
  • Chris M. Brown
    • 1
    Email author
  1. 1.Department of BiochemistryUniversity of OtagoDunedinNew Zealand
  2. 2.Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand

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