CasOT: a genome-wide Cas9/gRNA off-target searching tool

An Xiao; Zhenchao Cheng; Lei Kong; Zuoyan Zhu; Shuo Lin; Ge Gao; Bo Zhang

doi:10.1093/bioinformatics/btt764

CasOT: a genome-wide Cas9/gRNA off-target searching tool

Bioinformatics. 2014 Apr 15;30(8):1180-1182. doi: 10.1093/bioinformatics/btt764. Epub 2014 Jan 2.

Authors

An Xiao¹, Zhenchao Cheng¹, Lei Kong¹, Zuoyan Zhu¹, Shuo Lin¹, Ge Gao¹, Bo Zhang¹

Affiliation

¹ Key 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.

PMID: 24389662
DOI: 10.1093/bioinformatics/btt764

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.

MeSH terms

CRISPR-Cas Systems*
Computational Biology / methods*
Gene Targeting
Humans
RNA, Guide, CRISPR-Cas Systems / genetics*
Software*

Substances

RNA, Guide, CRISPR-Cas Systems