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Updated: May 4, 2026

CIRCLE-Seq for Interrogation of Off-Target Gene Editing
Published on: November 1, 2024
CasOT: a genome-wide Cas9/gRNA off-target searching tool
An Xiao1, Zhenchao Cheng1, Lei Kong1
1Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Abstract:
The CRISPR/Cas or Cas9/guide RNA system is a newly developed, easily engineered and highly effective tool for gene targeting; it has considerable off-target effects in cultured human cells and in several organisms. However, the Cas9/guide RNA target site is too short for existing alignment tools to exhaustively and effectively identify potential off-target sites. CasOT is a local tool designed to find potential off-target sites in any given genome or user-provided sequence, with user-specified types of protospacer adjacent motif, and number of mismatches allowed in the seed and non-seed regions.
Availability:
http://eendb.zfgenetics.org/casot/ CONTACT: zfgenetics@gmail.com or bzhang@pku.edu.cn Supplementary Information: Supplementary data are available at Bioinformatics online.
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