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CRISPRCasFinder is a tool to find CRISPR (clustered regularly interspaced short palindromic repeats) arrays and detect Cas proteins. The CRISPRCasFinder algorithm aids validation using a rating system, predicts the orientation of CRISPRs, and detects and types Cas protein based on the latest classification.


Model organisms; Transcription factors and regulatory sites; Sequence composition, complexity and repeats; DNA polymorphism; Gene expression


  • Operation: Repeat sequence detection; Sequence motif recognition; Clustering; Repeat sequence analysis
  • Input: FASTA
  • Output: -
  • Software interface: Command-line user interface; Web user interface
  • Language: Perl
  • Operating system: Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 4.2.20
  • Maturity: Mature
  • Credit: Institut Français de Bioinformatique (IFB), European Defense Agency Research and Technology project Bioforensics for Biodefence, ANR.
  • Contact: (General) christine.pourcel _at_ | (Technical) pierre-albert.charbit _at_ | mtouchon _at_
  • Collection: -


Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C "CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins." Nucleic Acids Res. 2018; 46(W1):W246-W251
PMID: 29790974
PMCID: PMC6030898

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