Sangsu Bae1,2,4,*, Jeongbin Park3,4 and Jin-Soo Kim1,2,*
1National Creative Research Initiatives Center for Genome Engineering, 2Department of Chemistry, Seoul National University, Seoul, South Korea, 3Department of Physics and Astronomy, Seoul National University, Seoul, South Korea
*To whom correspondence should be addressed. Sangsu BAE, Jin-Soo Kim
Summary: The Type II 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 (PAM) sequences recognized by Cas9, the essential protein component in RGENs. Cas-OFFinder is available as a command-line program or accessible via our website.