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

• Published in: Bioinformatics Vol. 30; no. 10; pp. 1473 - 1475
• Main Authors: Bae, Sangsu, Park, Jeongbin, Kim, Jin-Soo
• Format: Journal Article
• Language: English
• 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
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btu048

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