{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T10:00:59Z","timestamp":1781690459675,"version":"3.54.5"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2018,5,22]],"date-time":"2018-05-22T00:00:00Z","timestamp":1526947200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Institut Fran\u00e7ais de Bioinformatique","award":["ANR-11-INSB-0013"],"award-info":[{"award-number":["ANR-11-INSB-0013"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,2]]},"DOI":"10.1093\/nar\/gky425","type":"journal-article","created":{"date-parts":[[2018,5,9]],"date-time":"2018-05-09T15:13:27Z","timestamp":1525878807000},"page":"W246-W251","source":"Crossref","is-referenced-by-count":1474,"title":["CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins"],"prefix":"10.1093","volume":"46","author":[{"given":"David","family":"Couvin","sequence":"first","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Universit\u00e9 Paris-Saclay, 91198 Gif-sur-Yvette, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aude","family":"Bernheim","sequence":"additional","affiliation":[{"name":"Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, Paris, France"},{"name":"CNRS, UMR3525, 25-28 rue du Docteur Roux, 75015, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Toffano-Nioche","sequence":"additional","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Universit\u00e9 Paris-Saclay, 91198 Gif-sur-Yvette, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Touchon","sequence":"additional","affiliation":[{"name":"Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, Paris, France"},{"name":"CNRS, UMR3525, 25-28 rue du Docteur Roux, 75015, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juraj","family":"Michalik","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Lille 1, CRIStAL, \u00e9quipe Bonsai, Cit\u00e9 Scientifique Bat M3, 59655 Villeneuve d\u2019Ascq Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bertrand","family":"N\u00e9ron","sequence":"additional","affiliation":[{"name":"Bioinformatics and Biostatistics Hub \u2013 C3BI, USR 3756 IP CNRS \u2013 Paris, Institut Pasteur, 25\u201328 rue du Docteur Roux, 75015, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7704-822X","authenticated-orcid":false,"given":"Eduardo P C","family":"Rocha","sequence":"additional","affiliation":[{"name":"Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, Paris, France"},{"name":"CNRS, UMR3525, 25-28 rue du Docteur Roux, 75015, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilles","family":"Vergnaud","sequence":"additional","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Universit\u00e9 Paris-Saclay, 91198 Gif-sur-Yvette, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Gautheret","sequence":"additional","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Universit\u00e9 Paris-Saclay, 91198 Gif-sur-Yvette, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Pourcel","sequence":"additional","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Universit\u00e9 Paris-Saclay, 91198 Gif-sur-Yvette, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,5,22]]},"reference":[{"key":"key\n\t\t\t\t20180630062749_B1","first-page":"7536","article-title":"Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus","volume":"99","author":"Tang","year":"2002","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t20180630062749_B2","first-page":"722","article-title":"An updated evolutionary classification of CRISPR-Cas systems","volume":"13","author":"Makarova","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"key\n\t\t\t\t20180630062749_B3","first-page":"385","article-title":"Discovery and functional characterization of diverse class 2 CRISPR-Cas systems","volume":"60","author":"Shmakov","year":"2015","journal-title":"Mol. Cell"},{"key":"key\n\t\t\t\t20180630062749_B4","first-page":"933","article-title":"Applications of CRISPR technologies in research and beyond","volume":"34","author":"Barrangou","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t20180630062749_B5","first-page":"20150496","article-title":"CRISPR-Cas: biology, mechanisms and relevance","volume":"371","author":"Hille","year":"2016","journal-title":"Philos. Trans. R Soc. Lond. B Biol. Sci."},{"key":"key\n\t\t\t\t20180630062749_B6","first-page":"105","article-title":"Clustered regularly interspaced short palindromic repeats (CRISPRs) for the genotyping of bacterial pathogens","volume":"551","author":"Grissa","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"key\n\t\t\t\t20180630062749_B7","first-page":"W52","article-title":"CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats","volume":"35","author":"Grissa","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062749_B8","first-page":"209","article-title":"CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats","volume":"8","author":"Bland","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180630062749_B9","first-page":"18","article-title":"PILER-CR: fast and accurate identification of CRISPR repeats","volume":"8","author":"Edgar","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180630062749_B10","first-page":"356","article-title":"CRISPRDetect: a flexible algorithm to define CRISPR arrays","volume":"17","author":"Biswas","year":"2016","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180630062749_B11","first-page":"32942","article-title":"CRISPRdigger: detecting CRISPRs with better direct repeat annotations","volume":"6","author":"Ge","year":"2016","journal-title":"Sci. Rep."},{"key":"key\n\t\t\t\t20180630062749_B12","first-page":"e3219","article-title":"CRF: detection of CRISPR arrays using random forest","volume":"5","author":"Wang","year":"2017","journal-title":"PeerJ"},{"key":"key\n\t\t\t\t20180630062749_B13","first-page":"1805","article-title":"Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs","volume":"30","author":"Biswas","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630062749_B14","first-page":"8034","article-title":"CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems","volume":"41","author":"Lange","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062749_B15","first-page":"i489","article-title":"CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci","volume":"30","author":"Alkhnbashi","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630062749_B16","first-page":"i576","article-title":"Characterizing leader sequences of CRISPR loci","volume":"32","author":"Alkhnbashi","year":"2016","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630062749_B17","first-page":"e110726","article-title":"MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems","volume":"9","author":"Abby","year":"2014","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20180630062749_B18","article-title":"HMMCAS: a web tool for the identification and domain annotations of Cas proteins","author":"Chai","year":"2017","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"key\n\t\t\t\t20180630062749_B19","first-page":"92","article-title":"Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements","volume":"18","author":"Zhang","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180630062749_B20","article-title":"CRISPRdisco: an automated pipeline for the discovery and analysis of CRISPR-Cas systems","volume":"1","author":"Crawley","year":"2018","journal-title":"CRISPR J."},{"key":"key\n\t\t\t\t20180630062749_B21","first-page":"53","article-title":"Replacing suffix trees with enhanced suffix arrays","volume":"2","author":"Abouelhoda","year":"2004","journal-title":"J. Discrete Algorithms"},{"key":"key\n\t\t\t\t20180630062749_B22","first-page":"653","article-title":"CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies","volume":"151","author":"Pourcel","year":"2005","journal-title":"Microbiology"},{"key":"key\n\t\t\t\t20180630062749_B23","first-page":"172","article-title":"The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats","volume":"8","author":"Grissa","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180630062749_B24","first-page":"1925","article-title":"The contribution of genetic recombination to CRISPR array evolution","volume":"7","author":"Kupczok","year":"2015","journal-title":"Genome Biol. Evol."},{"key":"key\n\t\t\t\t20180630062749_B25","first-page":"1565","article-title":"Identification of genes that are associated with DNA repeats in prokaryotes","volume":"43","author":"Jansen","year":"2002","journal-title":"Mol. Microbiol."},{"key":"key\n\t\t\t\t20180630062749_B26","first-page":"119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180630062749_B27","first-page":"67","article-title":"Diversity, classification and evolution of CRISPR-Cas systems","volume":"37","author":"Koonin","year":"2017","journal-title":"Curr. Opin. Microbiol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/46\/W1\/W246\/25110298\/gky425.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,6,30]],"date-time":"2018-06-30T06:28:04Z","timestamp":1530340084000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/46\/W1\/W246\/5001162"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,5,22]]},"references-count":27,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2018,5,22]]},"published-print":{"date-parts":[[2018,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gky425","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,7,2]]},"published":{"date-parts":[[2018,5,22]]}}}