CRISPR · Software
CRISPRCasFinder
Identifies CRISPR arrays and neighbouring Cas genes in genome sequences for researchers.
What CRISPRCasFinder is
CRISPRCasFinder is a bioinformatics tool created to detect CRISPR arrays—clustered regularly interspaced short palindromic repeats—and their associated Cas (CRISPR-associated) genes in genomic data. Developed by David Couvin, Christine Pourcel, and collaborators, it represents an updated and integrated successor to the earlier CRISPRFinder and CasFinder tools.
The software addresses the need to detect both repetitive CRISPR loci and the nearby protein-coding Cas genes that constitute functional CRISPR-Cas immune systems. By combining array detection with Cas protein discovery in a unified environment, it enables researchers to analyse microbial genomes without running separate pipelines.
How it works
CRISPRCasFinder operates as a Perl-based pipeline that accepts genomic sequences in FASTA format. It detects CRISPR repeat-spacer arrays and uses the MacSyFinder engine coupled with CASFinder models to mine the neighbouring genomic regions for Cas molecular systems.
The pipeline draws on supplementary reference datasets, including repeat lists and repeat-direction definitions, to characterise array orientations and identify the specific Cas gene components present in the sequence.
Key facts
- Input format
- FASTA nucleotide sequence
- Core language
- Perl
- Integrated tools
- MacSyFinder, CASFinder, CRISPRFinder, CasFinder, Vmatch
- Documentation
- CRISPRCasFinder_Viewer_manual.pdf
What you can use it for
- CRISPR array detection
- Locating clustered regularly interspaced short palindromic repeat arrays within FASTA-formatted genomic sequences.
- Cas gene discovery
- Mining regions surrounding CRISPR loci to identify Cas protein-coding genes.
- CRISPR-Cas system annotation
- Simultaneously characterising both repeat arrays and Cas gene complexes to identify complete CRISPR-Cas molecular systems.
Run it here
The research agent sets CRISPRCasFinder up on its machine the first time a task needs it, then runs it and reads the output back to you. Nothing to install on your side.
Try asking
“Run CRISPRCasFinder on this genome and report the CRISPR-Cas systems.”
Strengths and limits
Good at
- Combines CRISPR array detection and Cas protein identification within a single automated pipeline.
- Integrates MacSyFinder and CASFinder models to search for molecular systems directly from sequence data.
- Available as a standalone Perl pipeline or a containerised Singularity image.
Watch out for
- Requires specific Perl CPAN module dependencies, such as Date::Calc, which may necessitate manual configuration.
- Relies on external bundled tools, including Vmatch and MacSyFinder, to complete its search workflow.
Questions
Can I run CRISPRCasFinder online without installing it?
The research agent sets CRISPRCasFinder up on its machine the first time a task needs it, then runs it and reads the output back to you. Nothing to install on your side.
What licence is CRISPRCasFinder under?
GPL-3.0. The terms are published at https://crisprcas.i2bc.paris-saclay.fr/.
What sequence format is required for CRISPRCasFinder?
The program accepts input sequence data in FASTA format.
How does CRISPRCasFinder identify Cas genes?
It integrates the MacSyFinder program and CASFinder models to search for and annotate Cas genes around CRISPR arrays.
How does CRISPRCasFinder differ from CRISPRFinder?
It is an updated version that integrates CasFinder into the workflow, allowing users to search for both CRISPR arrays and Cas proteins simultaneously.
How to cite it
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 Jul 2;46(W1):W246-W251. DOI: https://doi.org/10.1093/nar/gky425 [PMID:29790974]
Written from CRISPRCasFinder's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.