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.


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

Contact: or

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

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


  • RNA, Guide