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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 12, Issue 1

Issues

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

Dayong Guo
  • Corresponding author
  • Syncbiotech Co. Ltd, 12 Xuefu Rd, High-tech District, Nanjing, China
  • Model Animal Research Center, Nanjing University, Nanjing, China
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Xiaojing Li / Pan Zhu / Yanrong Feng / Juan Yang / Zhihong Zheng
  • Key Laboratory of Transgenic Animal Research, Laboratory Animal Center of Liaoning Province, China Medical University, Shenyang, China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Wei Yang
  • Key Laboratory of Transgenic Animal Research, Laboratory Animal Center of Liaoning Province, China Medical University, Shenyang, China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Enuo Zhang
  • Key Laboratory of Transgenic Animal Research, Laboratory Animal Center of Liaoning Province, China Medical University, Shenyang, China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Shenglai Zhou
  • Key Laboratory of Transgenic Animal Research, Laboratory Animal Center of Liaoning Province, China Medical University, Shenyang, China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Hongyu Wang
  • Syncbiotech Co. Ltd, 12 Xuefu Rd, High-tech District, Nanjing, China
  • Model Animal Research Center, Nanjing University, Nanjing, China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2015-283

Summary

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 (http://cas9.wicp.net) has established a speedy, accurate, flexible and high through-put computational gene knockout pipeline supporting the sequence-specific endonuclease induced mutagenesis.

About the article

Published Online: 2016-10-18

Published in Print: 2015-03-01


Citation Information: Journal of Integrative Bioinformatics, Volume 12, Issue 1, Pages 35–48, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2015-283.

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© 2015 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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