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


METHODS
Cas-OFFinder free access at http://www.rgenome.net/cas-offinder.


BACKGROUND
baesau@snu.ac.kr or jskim01@snu.ac.kr.
National Creative Research Initiatives Center for Genome Engineering, Department of Chemistry and Department of Physics and Astronomy, Seoul National University, 599 Gwanak-ro, Seoul 151-742, South Korea.
Sangsu
S
Bae
Jeongbin
J
Park
Jin-Soo
JS
Kim
D000465:Algorithms; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D001483:Base Sequence; D000076987:CRISPR-Associated Protein 9; D004247:DNA / Q000235:genetics / Q000378:metabolism; D004720:Endonucleases / Q000737:chemistry* / Q000235:genetics; D015894:Genome, Human; D018745:Genome, Plant; D006801:Humans; D051379:Mice; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013997:Time Factors; D058727:RNA, Small Untranslated
D001426:Bacterial Proteins; D004247:DNA; D000076987:CRISPR-Associated Protein 9; C000606107:Cas9 endonuclease Streptococcus pyogenes; D004720:Endonucleases; D058727:RNA, Small Untranslated