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CRISPR pp 77–89Cite as

Computational Detection of CRISPR/crRNA Targets

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Part of the Methods in Molecular Biology book series (MIMB,volume 1311)

Abstract

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

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Acknowledgements

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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Correspondence to Chris M. Brown .

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Biswas, A., Fineran, P.C., Brown, C.M. (2015). Computational Detection of CRISPR/crRNA Targets. In: Lundgren, M., Charpentier, E., Fineran, P. (eds) CRISPR. Methods in Molecular Biology, vol 1311. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2687-9_5

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  • DOI: https://doi.org/10.1007/978-1-4939-2687-9_5

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2686-2

  • Online ISBN: 978-1-4939-2687-9

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