Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9

Jeongbin Park; Jin-Soo Kim; Sangsu Bae

doi:10.1093/bioinformatics/btw103

Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9

Bioinformatics. 2016 Jul 1;32(13):2017-23. doi: 10.1093/bioinformatics/btw103. Epub 2016 Feb 24.

Authors

Jeongbin Park¹, Jin-Soo Kim², Sangsu Bae³

Affiliations

¹ Department of Chemistry, Hanyang University, Seoul 133-791, South Korea.
² Center for Genome Engineering, Institute for Basic Science, Seoul 151-747, South Korea Department of Chemistry, Seoul National University, Seoul 151-747, South Korea.
³ Department of Chemistry, Hanyang University, Seoul 133-791, South Korea Institute for Materials Design, Hanyang University, Seoul 133-791, South Korea.

Abstract

Motivation: CRISPR-derived RNA guided endonucleases (RGENs) have been widely used for both gene knockout and knock-in at the level of single or multiple genes. RGENs are now available for forward genetic screens at genome scale, but single guide RNA (sgRNA) selection at this scale is difficult.

Results: We develop an online tool, Cas-Database, a genome-wide gRNA library design tool for Cas9 nucleases from Streptococcus pyogenes (SpCas9). With an easy-to-use web interface, Cas-Database allows users to select optimal target sequences simply by changing the filtering conditions. Furthermore, it provides a powerful way to select multiple optimal target sequences from thousands of genes at once for the creation of a genome-wide library. Cas-Database also provides a web application programming interface (web API) for advanced bioinformatics users.

Availability and implementation: Free access at http://www.rgenome.net/cas-database/

Contact: sangsubae@hanyang.ac.kr or jskim01@snu.ac.kr

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

CRISPR-Cas Systems*
Databases, Genetic*
Gene Knockout Techniques*
Gene Library*
Internet
RNA, Guide, CRISPR-Cas Systems / genetics*
Streptococcus pyogenes / enzymology

Substances

RNA, Guide, CRISPR-Cas Systems