Author:David Couvin, Aude Bernheim, Claire Toffano-Nioche, Marie Touchon, Juraj Michalik, Bertrand Néron, Eduardo P. C. Rocha, Gilles Vergnaud, Daniel Gautheret, Christine Pourcel
Pages:6
Summary:CRISPRCasFinder is an updated version of CRISPRFinder and CasFinder, designed to identify both CRISPR arrays and Cas proteins. The program includes enhanced CRISPR array detection tools, a rating system for evidence levels, and improved orientation prediction. It also features an updated Cas protein detection and typing tool that aligns with the latest classification scheme. CRISPRCasFinder is available as both a web server and a standalone Linux-compatible program. The web server accepts multi-Fasta DNA sequence files up to 50 Mb in size, while the standalone version has no predefined input size limit. The program outputs results in various formats, including .xls, GFF3, JSON, TSV, and Fasta. The evaluation of CRISPR and Cas detection using a test panel of 400 genomic sequences showed that CRISPRCasFinder performed similarly to other programs like PILER-CR, CRT, and CRISPRDetect. The program's performance was further validated through use case studies, demonstrating its ability to accurately identify CRISPR and Cas loci. CRISPRCasFinder is expected to evolve to improve CRISPR array orientation prediction and to incorporate novel typing methods for Cas systems.