GuideScan software for improved single and paired CRISPR guide RNA design

Nat Biotechnol. 2017 Apr;35(4):347-349. doi: 10.1038/nbt.3804. Epub 2017 Mar 6.


We present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. We also show that the trie data structure of GuideScan enables the design of gRNAs that are more specific than those designed by existing tools.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • CRISPR-Cas Systems / genetics
  • Chromosome Mapping / methods
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
  • Gene Silencing*
  • Machine Learning*
  • RNA, Small Interfering / genetics*
  • Sequence Analysis, RNA / methods
  • Software*


  • RNA, Small Interfering