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Review of CRISPR/Cas9 sgRNA Design Tools

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Abstract

The adaptive immunity system in bacteria and archaea, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-associate (CRISPR/Cas), has been adapted as a powerful gene editing tool and got a broad application in genome research field due to its ease of use and cost-effectiveness. The performance of CRISPR/Cas relies on well-designed single-guide RNA (sgRNA), so a lot of bioinformatic tools have been developed to assist the design of highly active and specific sgRNA. These tools vary in design specifications, parameters, genomes and so on. To help researchers to choose their proper tools, we reviewed various sgRNA design tools, mainly focusing on their on-target efficiency prediction model and off-target detection algorithm.

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Acknowledgements

We would like thank to Jingyu Amy Peng and Chen-Hao Chen from Harvard T.H. Chan School of Public Health, Shenglin Mei and Jian Ma from Tongji University for their discussion about this work. This work was supported by National Key R&D Program of China 2017YFB0202602, 2017YFC1311003, 2016YFC1302500, 2016YFB0200400, 2017YFB0202104; NSFC Grants 61772543, U1435222, 61625202, 61272056; the Funds of State Key Laboratory of Chemo/Biosensing and Chemometrics; the Fundamental Research Funds for the Central Universities; and Guangdong Provincial Department of Science and Technology under grant No. 2016B090918122.

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  1. Yingbo Cui and Jiaming Xu are equal contributors.

Authors and Affiliations

  1. College of Computer, National University of Defense Technology, Changsha, 410073, China

    Yingbo Cui, Jiaming Xu, Xiangke Liao & Shaoliang Peng

  2. College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China

    Minxia Cheng & Shaoliang Peng

  3. National Supercomputing Center in Changsha, Changsha, 410082, China

    Shaoliang Peng

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Cui, Y., Xu, J., Cheng, M. et al. Review of CRISPR/Cas9 sgRNA Design Tools. Interdiscip Sci Comput Life Sci 10, 455–465 (2018). https://doi.org/10.1007/s12539-018-0298-z

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