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CHOPCHOP is a web-based tool to select target sites for CRISPR/Cas9- or TALEN-directed mutagenesis. The CHOPCHOP algorithm predicts off-target binding of single-guide RNAs (sgRNAs) and TALENs using effective sequence alignment methods and visualizes the candidate target sites, restriction sites, primer candidates, together with color-coded quality scores.


Sequence analysis


  • Operation: Prediction and recognition
  • Software interface: Web user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Other
  • Cost: Free for academic use
  • Version name: 3.0.0
  • Credit: National Defense Science and Engineering Graduate Fellowship, American Cancer Society, Human Frontier Science Program, National Human, Genome Research Institute (NHGRI) Center for Excellence in Genomics Science.
  • Contact: kornel.labun _at_ | tessa.montague _at_
  • Collection: -


Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E "CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing." Nucleic Acids Res. 2014; 42(Web Server issue):W401-7
PMID: 24861617
PMCID: PMC4086086

Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E "CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering." Nucleic Acids Res, 2016
PMID: 27185894
PMCID: PMC4987937

Labun K, Montague TG, Krause M, Torres Cleuren YN, Tjeldnes H, Valen E "CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing." Nucleic Acids Res, 2019
PMID: 31106371
PMCID: PMC6602426

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