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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.
Affiliation
  • Couvin D; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
  • Bernheim A; Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, Paris, France.
  • Toffano-Nioche C; CNRS, UMR3525, 25-28 rue du Docteur Roux, 75015, Paris, France.
  • Touchon M; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
  • Michalik J; Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, Paris, France.
  • Néron B; CNRS, UMR3525, 25-28 rue du Docteur Roux, 75015, Paris, France.
  • Rocha EPC; Université Lille 1, CRIStAL, équipe Bonsai, Cité Scientifique Bat M3, 59655 Villeneuve d'Ascq Cedex, France.
  • Vergnaud G; Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS - Paris, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, France.
  • Gautheret D; Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, Paris, France.
  • Pourcel C; CNRS, UMR3525, 25-28 rue du Docteur Roux, 75015, Paris, France.
Nucleic Acids Res ; 46(W1): W246-W251, 2018 07 02.
Article in En | MEDLINE | ID: mdl-29790974
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / CRISPR-Associated Proteins / Clustered Regularly Interspaced Short Palindromic Repeats Language: En Journal: Nucleic Acids Res Year: 2018 Document type: Article Affiliation country: Francia
Fulltext
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / CRISPR-Associated Proteins / Clustered Regularly Interspaced Short Palindromic Repeats Language: En Journal: Nucleic Acids Res Year: 2018 Document type: Article Affiliation country: Francia