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© ALPS team
Publication : Nucleic acids research

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

Team: Expertise group : ALPS – Algorithmics and programming in science
Team: Bioinformatics and Biostatistics HUB
Team: Microbial Evolutionary Genomics
Member: Bertrand Néron
Member: Marie Touchon
Member: Eduardo Rocha
Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Nucleic acids research - 02 Jul 2018

Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C

Link to Pubmed [PMID] – 29790974

Nucleic Acids Res. 2018 Jul;46(W1):W246-W251

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.