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BY-NC-ND 4.0 license Open Access Published by De Gruyter October 18, 2016

Online High-throughput Mutagenesis Designer Using Scoring Matrix of Sequence-specific Endonucleases

  • Dayong Guo EMAIL logo , Xiaojing Li , Pan Zhu , Yanrong Feng , Juan Yang , Zhihong Zheng , Wei Yang , Enuo Zhang , Shenglai Zhou and Hongyu Wang


CRISPR Cas9 and other sequence-specific endonucleases are fundamental genome editors supporting gene knockout and gene therapy. A speedy and accurate computational allele designer is required for a high through-put gene mutagenesis pipeline using these new techniques.

An automatic system, Cas9 online designer (COD), was created to screen Cas9 targets and off-targets, as well as to provide gene knockout and genotyping strategies. A gene knockout rat model was successfully created and genotyped under the direction of this online system confirming its ability to predict real targets and off-targets. Gene knockout strategies to mutate 72 rat cytochrome P450 genes were designed instantly by the system to demonstrate its high-throughput efficiency. Also, the system used an off-target scoring matrix which can be applied to any sequence-specific genome editing tools besides Cas9.

The COD system ( has established a speedy, accurate, flexible and high through-put computational gene knockout pipeline supporting the sequence-specific endonuclease induced mutagenesis.

Published Online: 2016-10-18
Published in Print: 2015-3-1

© 2015 The Author(s). Published by Journal of Integrative Bioinformatics.

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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