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. 2014 May 15;30(10):1473-5.
doi: 10.1093/bioinformatics/btu048. Epub 2014 Jan 24.

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

Sangsu Bae  1 , Jeongbin Park, Jin-Soo Kim
Affiliations

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

Sangsu Bae et al. Bioinformatics. .

Abstract

Summary: The Type II clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system is an adaptive immune response in prokaryotes, protecting host cells against invading phages or plasmids by cleaving these foreign DNA species in a targeted manner. CRISPR/Cas-derived RNA-guided engineered nucleases (RGENs) enable genome editing in cultured cells, animals and plants, but are limited by off-target mutations. Here, we present a novel algorithm termed Cas-OFFinder that searches for potential off-target sites in a given genome or user-defined sequences. Unlike other algorithms currently available for identification of RGEN off-target sites, Cas-OFFinder is not limited by the number of mismatches and allows variations in protospacer-adjacent motif sequences recognized by Cas9, the essential protein component in RGENs. Cas-OFFinder is available as a command-line program or accessible via our website.

Availability and implementation: Cas-OFFinder free access at http://www.rgenome.net/cas-offinder.

Contact: baesau@snu.ac.kr or jskim01@snu.ac.kr.

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Figures

Fig. 1.
Fig. 1.
(A) The scheme of Cas-OFFinder. (B) The workflow of Cas-OFFinder. (C) Running time per target site as a function of the number of input target sites via CPU (black squares) and GPU (red circles)
See this image and copyright information in PMC

References

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