CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization

Houxiang Zhu; Lauren Misel; Mitchell Graham; Michael L Robinson; Chun Liang

doi:10.1038/srep25516

CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization

Sci Rep. 2016 May 23:6:25516. doi: 10.1038/srep25516.

Authors

Houxiang Zhu¹, Lauren Misel¹, Mitchell Graham¹, Michael L Robinson¹, Chun Liang^{1

2}

Affiliations

¹ Department of Biology, Miami University, Oxford, Ohio, 45056, USA.
² Department of Software Engineering, Miami University, Oxford, Ohio 45056, USA.

Abstract

The CRISPR system holds much promise for successful genome engineering, but therapeutic, industrial, and research applications will place high demand on improving the specificity and efficiency of this tool. CT-Finder (http://bioinfolab.miamioh.edu/ct-finder) is a web service to help users design guide RNAs (gRNAs) optimized for specificity. CT-Finder accommodates the original single-gRNA Cas9 system and two specificity-enhancing paired-gRNA systems: Cas9 D10A nickases (Cas9n) and dimeric RNA-guided FokI nucleases (RFNs). Optimal target candidates can be chosen based on the minimization of predicted off-target effects. Graphical visualization of on-target and off-target sites in the genome is provided for target validation. Major model organisms are covered by this web service.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

CRISPR-Cas Systems*
Clustered Regularly Interspaced Short Palindromic Repeats*
Computational Biology / methods*
Databases, Genetic*
Gene Editing*
Gene Targeting
RNA, Guide, CRISPR-Cas Systems / genetics
Software*
User-Computer Interface
Web Browser

Substances

RNA, Guide, CRISPR-Cas Systems

Grants and funding

R01 EY012995/EY/NEI NIH HHS/United States