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

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 nucl...

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Published inBioinformatics Vol. 30; no. 10; pp. 1473 - 1475
Main Authors Bae, Sangsu, Park, Jeongbin, Kim, Jin-Soo
Format Journal Article
LanguageEnglish
Published England Oxford University Press 15.05.2014
Subjects
Algorithms
Animals
Applications Notes
Bacterial Proteins - chemistry
Bacterial Proteins - genetics
Base Sequence
DNA - genetics
DNA - metabolism
Endonucleases - chemistry
Endonucleases - genetics
Genome, Human
Genome, Plant
Humans
Mice
RNA, Guide - genetics
RNA, Guide - metabolism
Sequence Analysis, DNA - methods
Software
Time Factors
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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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Associate Editor: John Hancock
The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.
ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btu048