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Int J Biol Sci 2017; 13(12):1470-1478. doi:10.7150/ijbs.21312

Research Paper

CRISPR-offinder: a CRISPR guide RNA design and off-target searching tool for user-defined protospacer adjacent motif

Changzhi Zhao1,2*, Xiaoguo Zheng3,4*, Wubin Qu5*, Guanglei Li1, Xinyun Li1,2, Yi-Liang Miao1,2, Xiaosong Han1, Xiangdong Liu1,2, Zhenhua Li3,4, Yunlong Ma1, Qianzhi Shao5, Haiwei Li5, Fei Sun3,4✉, Shengsong Xie1,2✉, Shuhong Zhao1,2✉

1. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China;
2. The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, P. R. China;
3. The International Peace Maternity & Child Health Hospital of China Welfare Institute (IPMCH), Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China;
4. Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China;
5. iGeneTech Bioscience Co., Ltd., Beijing 102206, P. R. China.
* The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint first authors.

Abstract

Designing efficient and specific CRISPR single-guide RNAs (sgRNAs) is vital for the successful application of CRISPR technology. Currently, a growing number of new RNA-guided endonucleases with a different protospacer adjacent motif (PAM) have been discovered, suggesting the necessity to develop a versatile tool for designing sgRNA to meet the requirement of different RNA-guided DNA endonucleases. Here, we report the development of a flexible sgRNA design program named “CRISPR-offinder”. Support for user-defined PAM and sgRNA length was provided to increase the targeting range and specificity. Additionally, evaluation of on- and off-target scoring algorithms was integrated into the CRISPR-offinder. The CRISPR-offinder has provided the bench biologist a rapid and efficient tool for identification of high quality target sites, and it is freely available at https://sourceforge.net/projects/crispr-offinder-v1-2/ or http://www.biootools.com.

Keywords: genome editing, user-defined protospacer adjacent motif, off-target.

This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/). See http://ivyspring.com/terms for full terms and conditions.
How to cite this article:
Zhao C, Zheng X, Qu W, Li G, Li X, Miao YL, Han X, Liu X, Li Z, Ma Y, Shao Q, Li H, Sun F, Xie S, Zhao S. CRISPR-offinder: a CRISPR guide RNA design and off-target searching tool for user-defined protospacer adjacent motif. Int J Biol Sci 2017; 13(12):1470-1478. doi:10.7150/ijbs.21312. Available from http://www.ijbs.com/v13p1470.htm