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

• DOI: 10.1093/bioinformatics/btu048
• Publication Date: 2014-01-24T20:24:14Z
• Authors: Sangsu Bae; Jeongbin Park; Jin-Soo Kim
• Keywords: 0301 basic medicine; Time Factors; Base Sequence; Genome, Human; DNA; Sequence Analysis, DNA; Endonucleases; Applications Notes; 3. Good health; Mice; 03 medical and health sciences; Bacterial Proteins; CRISPR-Associated Protein 9; Animals; Humans; RNA, Small Untranslated; Algorithms; Genome, Plant; Software

AbstractSummary: 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: [e-mail] or [e-mail]