Find CRISPR arrays and Cas systems in a genome

Add a FASTA file and run. Detection happens in this tab; the sequence is never uploaded.

Sequence

Or paste FASTA

Options

CRISPR arrays

Minimum repeat length

Maximum repeat length

Minimum spacer length

Maximum spacer length

Minimum spacer count

Minimum evidence level (1–4)

No mismatches Repeats must match each other exactly.

Cas systems

Detect Cas systems Genetic code 11. The command-line tool supports other codes. Metagenome mode Metagenomic gene prediction for every sequence.

Results

No results yet CRISPR arrays and Cas systems will be listed here.

References

If you use this tool or the underlying algorithms, please cite:

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: 10.1093/nar/gky425 — PMID: 29790974
Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W52–7. DOI: 10.1093/nar/gkm360 — PMID: 17537822
Abby SS, Néron B, Ménager H, Touchon M, Rocha EP. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS One. 2014 Oct 17;9(10):e110726. DOI: 10.1371/journal.pone.0110726 — PMID: 25330359
Néron B, Denise R, Coluzzi C, Touchon M, Rocha EPC, Abby SS. MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes. Peer Community Journal, 2023. DOI: 10.1101/2022.09.02.506364