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Bioinformatics. 2015 Nov 15;31(22):3676-8. doi: 10.1093/bioinformatics/btv423. Epub 2015 Jul 23.

CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation.

Author information

1
Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China, Stanford Chemistry, Engineering & Medicine for Human Health (ChEM-H).
2
Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
3
Department of Bioengineering and.
4
Stanford Chemistry, Engineering & Medicine for Human Health (ChEM-H), Department of Bioengineering and Department of Chemical and Systems Biology, Stanford University, 443 Via Ortega, Shriram Center 376, Stanford, CA 94305-4125, USA.

Abstract

The CRISPR/Cas9 system was recently developed as a powerful and flexible technology for targeted genome engineering, including genome editing (altering the genetic sequence) and gene regulation (without altering the genetic sequence). These applications require the design of single guide RNAs (sgRNAs) that are efficient and specific. However, this remains challenging, as it requires the consideration of many criteria. Several sgRNA design tools have been developed for gene editing, but currently there is no tool for the design of sgRNAs for gene regulation. With accumulating experimental data on the use of CRISPR/Cas9 for gene editing and regulation, we implement a comprehensive computational tool based on a set of sgRNA design rules summarized from these published reports. We report a genome-wide sgRNA design tool and provide an online website for predicting sgRNAs that are efficient and specific. We name the tool CRISPR-ERA, for clustered regularly interspaced short palindromic repeat-mediated editing, repression, and activation (ERA).

AVAILABILITY AND IMPLEMENTATION:

http://CRISPR-ERA.stanford.edu.

CONTACT:

stanley.qi@stanford.edu or xwwang@tsinghua.edu.cn

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26209430
PMCID:
PMC4757951
DOI:
10.1093/bioinformatics/btv423
[Indexed for MEDLINE]
Free PMC Article

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