CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites

Bioinformatics. 2015 Apr 1;31(7):1120-3. doi: 10.1093/bioinformatics/btu743. Epub 2014 Nov 20.


CRISPRdirect is a simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence. The CRISPR/Cas system is a promising technique for genome engineering which allows target-specific cleavage of genomic DNA guided by Cas9 nuclease in complex with a guide RNA (gRNA), that complementarily binds to a ∼ 20 nt targeted sequence. The target sequence requirements are twofold. First, the 5'-NGG protospacer adjacent motif (PAM) sequence must be located adjacent to the target sequence. Second, the target sequence should be specific within the entire genome in order to avoid off-target editing. CRISPRdirect enables users to easily select rational target sequences with minimized off-target sites by performing exhaustive searches against genomic sequences. The server currently incorporates the genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast.

Availability: Freely available at

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • CRISPR-Cas Systems*
  • DNA / metabolism
  • Drug Design*
  • Endonucleases / metabolism
  • Gene Expression Regulation
  • Genome
  • Genomics / methods
  • Humans
  • Mice
  • Molecular Sequence Data
  • RNA Editing*
  • RNA, Guide / genetics*
  • Rats
  • Software*


  • RNA, Guide
  • DNA
  • Endonucleases