Related Experiment Video
Updated: May 3, 2026

CIRCLE-Seq for Interrogation of Off-Target Gene Editing
Published on: November 1, 2024
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided
Sangsu Bae1, Jeongbin Park, Jin-Soo Kim
1National 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.
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.
Related Concept Videos
CRISPR/Cas9 Genome Editing
CRISPR
CRISPR
Homologous Recombination
CRISPR and crRNAs
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
Conservative Site-specific Recombination and Phase Variation
The recognition sites for Cre recombinase called LoxP...

