Supplementary web site for

CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes


John Aach, Prashant Mali, George M. Church*


Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

*Correspondence should be addressed to


CRISPR/Cas9 systems enable many molecular activities to be efficiently directed to user-specifiable DNA sequences, including generation of dsDNA cuts and nicks, transcriptional activation and repression, and fluorescence. CRISPR targeting relies on base pairing of short RNA transcripts with their target DNA sequences that must also be adjacent to fixed DNA motifs. However, rules for Cas9 targeting specificity are incompletely known. With increasing numbers of Cas9 systems being developed and deployed in more and more organisms, there is now strong need for a flexible and rational method for finding Cas9 sites with low off-targeting potential. We address this through the CasFinder system, which we demonstrate by generating human and mouse exome-wide catalogs of specific sites for three varieties of Cas9 S. pyogenes, S. thermophilus (ST1), and N. meningitidis that each target 56-74% of all exons. We also generate reduced sets of up to 3 targets per gene for use in high-throughput Cas9-based gene knockout screens that target 75-80% of all genes.


         To download our article, go here.

         To download the CasFinder system, go here. Documentation on the program, its usage, and recommended customizations is provided in the Supplementary Information document published with our article on the bioRxiv web site indicated below. The CasFinder system is available under the OSI-compliant MIT license.

         To download the whole human and mouse exome Cas9 target site catalogs, and the reduced target sets for high-throughput gene-knockout screens, go here.

         If you use the CasFinder system or our exome site catalogs, please cite our article as:
Aach J, Mali P, Church GM. 2014. CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. bioRxiv doi: 10.1101/005074



Please contact John Aach with any questions or suggestions related to this material.


Last modified: 5/13/2014 6:42 AM