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CasFinder specifications


Unique identifier OMICS_11307
Name CasFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline George Church

Publication for CasFinder

CasFinder citations


A multi landing pad DNA integration platform for mammalian cell engineering

Nucleic Acids Res
PMCID: 5934685
PMID: 29617873
DOI: 10.1093/nar/gky216

[…] sequences for homologous recombination were derived from the public CHO-K1 genome database (,) based on the identified lentiviral integration sites. First, guide RNA sequences were designed using the CasFinder/CasValue algorithm or a CRISPR design tool such as () typically within 1 kb of the lentiviral integration sites. Then, 0.5–1 kb of genomic sequences 5′ and 3′ of the g […]


The lncRNA CASC15 regulates SOX4 expression in RUNX1 rearranged acute leukemia

Mol Cancer
PMCID: 5517805
PMID: 28724437
DOI: 10.1186/s12943-017-0692-x

[…] emove an internal BbsI restriction site. The 20-nt gRNA sequences flanking a 3.1–3.8 kb region (encompassing the first two exons) of mouse Casc15 (2610307P16Rik) were designed using sgRNA Scorer with CasFinder []. Detailed methods are available upon request. […]


A convenient method to pre screen candidate guide RNAs for CRISPR/Cas9 gene editing by NHEJ mediated integration of a ‘self cleaving’ GFP expression plasmid

PMCID: 5726473
PMID: 28679166
DOI: 10.1093/dnares/dsx029

[…] d off-targets in the mouse genome as assessed by e-CRISP Cas9 construct designer and had the best predicted efficiency by sgRNA Designer., From these, two candidates were picked that according to the CasFinder have no targets in the human genome and in 11 frequently employed model organisms (mouse, rat, cat, dog, pig, cow, chicken, zebrafish, C. elegans, Drosophila, and S. cerevisiae) thus, reserv […]


Inhibition of androgen receptor promotes CXC chemokine receptor 7 mediated prostate cancer cell survival

Sci Rep
PMCID: 5465216
PMID: 28596572
DOI: 10.1038/s41598-017-02918-3

[…] if (PAM) sequences were confirmed to be specific to CXCR7 (Basic Local Alignment Search Tool [BLAST] search; National Center for Biotechnology Information, Bethesda MD) and further confirmed with the CasFinder algorithm. Plasmids were transfected into cells using Lipofectamine 3000 Transfection Reagent (Invitrogen; L3000008). GFP positive cells were sorted using the BD FACSAria II (Augusta Univers […]


Biased and Unbiased Methods for the Detection of Off Target Cleavage by CRISPR/Cas9: An Overview

Int J Mol Sci
PMCID: 5037784
PMID: 27618019
DOI: 10.3390/ijms17091507

[…] to detect such sites. Systems such as the Cas-OF Finder (available online: [], the Feng Zhang lab’s Target Finder (available online:, the CasFinder (available online:, the CRISPR Design Tool ( [], E-CRISP (available online: [], an […]


Targeted and genome wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells

Nat Commun
PMCID: 4352754
PMID: 25425480
DOI: 10.1038/ncomms6507

[…] ion. To gauge the impact of SNVs on targets chosen in this manner, we analyzed a database of 927,104 specificity-checked Cas9 target sites in the human exome that had previously been generated by the CasFinder algorithm and identified for each target site all three-mismatch off-target sites genome-wide. For target sites selected this way we found a probability of 1.54% that SNVs in the PGP1 genome […]


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CasFinder institution(s)
Department of Genetics, Harvard Medical School, Boston, MA, USA
CasFinder funding source(s)
This work was supported by NIH grant P50 HG005550.

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