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

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 p...

Descripción completa

Detalles Bibliográficos
Autores principales: Couvin, David, Bernheim, Aude, Toffano-Nioche, Claire, Touchon, Marie, Michalik, Juraj, Néron, Bertrand, Rocha, Eduardo P C, Vergnaud, Gilles, Gautheret, Daniel, Pourcel, Christine
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Web Server Issue
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030898/
https://www.ncbi.nlm.nih.gov/pubmed/29790974
http://dx.doi.org/10.1093/nar/gky425
_version_ 1783337217260781568
author Couvin, David
Bernheim, Aude
Toffano-Nioche, Claire
Touchon, Marie
Michalik, Juraj
Néron, Bertrand
Rocha, Eduardo P C
Vergnaud, Gilles
Gautheret, Daniel
Pourcel, Christine
author_facet Couvin, David
Bernheim, Aude
Toffano-Nioche, Claire
Touchon, Marie
Michalik, Juraj
Néron, Bertrand
Rocha, Eduardo P C
Vergnaud, Gilles
Gautheret, Daniel
Pourcel, Christine
author_sort Couvin, David
collection PubMed
description 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.
format Online
Article
Text
id pubmed-6030898
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-60308982018-07-10 CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins Couvin, David Bernheim, Aude Toffano-Nioche, Claire Touchon, Marie Michalik, Juraj Néron, Bertrand Rocha, Eduardo P C Vergnaud, Gilles Gautheret, Daniel Pourcel, Christine Nucleic Acids Res Web Server Issue 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. Oxford University Press 2018-07-02 2018-05-22 /pmc/articles/PMC6030898/ /pubmed/29790974 http://dx.doi.org/10.1093/nar/gky425 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Couvin, David
Bernheim, Aude
Toffano-Nioche, Claire
Touchon, Marie
Michalik, Juraj
Néron, Bertrand
Rocha, Eduardo P C
Vergnaud, Gilles
Gautheret, Daniel
Pourcel, Christine
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
title CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
title_full CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
title_fullStr CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
title_full_unstemmed CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
title_short CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
title_sort crisprcasfinder, an update of crisrfinder, includes a portable version, enhanced performance and integrates search for cas proteins
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030898/
https://www.ncbi.nlm.nih.gov/pubmed/29790974
http://dx.doi.org/10.1093/nar/gky425
work_keys_str_mv AT couvindavid crisprcasfinderanupdateofcrisrfinderincludesaportableversionenhancedperformanceandintegratessearchforcasproteins
AT bernheimaude crisprcasfinderanupdateofcrisrfinderincludesaportableversionenhancedperformanceandintegratessearchforcasproteins
AT toffanoniocheclaire crisprcasfinderanupdateofcrisrfinderincludesaportableversionenhancedperformanceandintegratessearchforcasproteins
AT touchonmarie crisprcasfinderanupdateofcrisrfinderincludesaportableversionenhancedperformanceandintegratessearchforcasproteins
AT michalikjuraj crisprcasfinderanupdateofcrisrfinderincludesaportableversionenhancedperformanceandintegratessearchforcasproteins
AT neronbertrand crisprcasfinderanupdateofcrisrfinderincludesaportableversionenhancedperformanceandintegratessearchforcasproteins
AT rochaeduardopc crisprcasfinderanupdateofcrisrfinderincludesaportableversionenhancedperformanceandintegratessearchforcasproteins
AT vergnaudgilles crisprcasfinderanupdateofcrisrfinderincludesaportableversionenhancedperformanceandintegratessearchforcasproteins
AT gautheretdaniel crisprcasfinderanupdateofcrisrfinderincludesaportableversionenhancedperformanceandintegratessearchforcasproteins
AT pourcelchristine crisprcasfinderanupdateofcrisrfinderincludesaportableversionenhancedperformanceandintegratessearchforcasproteins

Ejemplares similares