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 firstname.lastname@example.org.
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
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
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.
modified: 5/13/2014 6:42 AM