CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

TLDR

CRISPR arrays and Cas proteins provide bacteria and archaea with adaptive immunity against mobile genetic elements such as phages and plasmids. CRISPRCasFinder enables simultaneous identification of CRISPR arrays and Cas proteins. The tool incorporates an enhanced array detector with a rating system, orientation prediction, and an updated Cas typing module, and is available both online and as a free, Linux‑compatible standalone application. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.

Abstract

CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.