Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites

Bioinformatics. 2015 Dec 15;31(24):4014-6. doi: 10.1093/bioinformatics/btv537. Epub 2015 Sep 10.


We present Cas-Designer, a user-friendly program to aid researchers in choosing appropriate target sites in a gene of interest for type II CRISPR/Cas-derived RNA-guided endonucleases, which are now widely used for biomedical research and biotechnology. Cas-Designer rapidly provides the list of all possible guide RNA sequences in a given input DNA sequence and their potential off-target sites including bulge-type sites in a genome of choice. In addition, the program assigns an out-of-frame score to each target site to help users choose appropriate sites for gene knockout. Cas-Designer shows the results in an interactive table and provides user-friendly filter functions.

Availability and implementation: Free access at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CRISPR-Associated Proteins*
  • CRISPR-Cas Systems*
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Endodeoxyribonucleases*
  • Gene Knockout Techniques*
  • Genome
  • Internet
  • RNA / chemistry
  • Sequence Analysis, DNA / methods*
  • Software*


  • CRISPR-Associated Proteins
  • RNA
  • Endodeoxyribonucleases