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

David Couvin; Aude Bernheim; Claire Toffano‐Nioche; Marie Touchon; Juraj Michálik; Bertrand Néron; Eduardo P. C. Rocha; Gilles Vergnaud; Daniel Gautheret; Christine Pourcel

doi:10.1093/nar/gky425

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.

Keywords

CRISPRBiologyPalindromeComputational biologyPlasmidSoftwareIdentification (biology)Mobile genetic elementsGeneticsComputer scienceOperating systemGene

MeSH Terms

CRISPR-Associated ProteinsCRISPR-Cas SystemsClustered Regularly Interspaced Short Palindromic RepeatsInternetSoftware

Affiliated Institutions

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Publication Info

Year: 2018
Type: article
Volume: 46
Issue: W1
Pages: W246-W251
Citations: 1444
Access: Closed

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APA Style

                            
                                
                                    David Couvin, 
                                
                                    Aude Bernheim, 
                                
                                    Claire Toffano‐Nioche
                                
                                et al.
                            
                            (2018). 
                            CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. 
                            Nucleic Acids Research
                            , 46
                            (W1)
                            , W246-W251.
                            https://doi.org/10.1093/nar/gky425
                        

Identifiers

DOI: 10.1093/nar/gky425
PMID: 29790974
PMCID: PMC6030898

Data Quality

Data completeness: 90%