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The identification of CRISPR loci is currently a non-standardized, ambiguous process, requiring the manual combination of multiple tools, where existing tools detect only parts of the CRISPR-systems, and lack quality control, annotation and assessment capabilities of the detected CRISPR loci. Our CRISPRloci server provides the first resource for the prediction and assessment of all possible CRISPR loci. The server integrates a series of advanced Machine Learning tools within a seamless web interface featuring: (i) prediction of all CRISPR arrays in the correct orientation; (ii) definition of CRISPR leaders for each locus; and (iii) annotation of cas genes and their unambiguous classification. As a result, CRISPRloci is able to accurately determine the CRISPR array and associated information, such as: the Cas subtypes; cassette boundaries; accuracy of the repeat structure, orientation and leader sequence; virus-host interactions; self-targeting; as well as the annotation of cas genes, all of which have been missing from existing tools. This annotation is presented in an interactive interface, making it easy for scientists to gain an overview of the CRISPR system in their organism of interest. Predictions are also rendered in GFF format, enabling in-depth genome browser inspection. In summary, CRISPRloci constitutes a full suite for CRISPR\u2013Cas system characterization that offers annotation quality previously available only after manual inspection.<\/jats:p>","DOI":"10.1093\/nar\/gkab456","type":"journal-article","created":{"date-parts":[[2021,5,17]],"date-time":"2021-05-17T19:17:58Z","timestamp":1621279078000},"page":"W125-W130","source":"Crossref","is-referenced-by-count":23,"title":["CRISPRloci:<\/tt>\u00a0comprehensive and accurate annotation of CRISPR\u2013Cas systems"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"http:\/\/orcid.org\/0000-0001-8088-590X","authenticated-orcid":false,"given":"Omer S","family":"Alkhnbashi","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany"}]},{"given":"Alexander","family":"Mitrofanov","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany"}]},{"given":"Robson","family":"Bonidia","sequence":"additional","affiliation":[{"name":"Institute of Mathematics and Computer Sciences, University of S\u00e3o Paulo, S\u00e3o Carlos, SP, Brazil"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-7926-5911","authenticated-orcid":false,"given":"Martin","family":"Raden","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-7357-4959","authenticated-orcid":false,"given":"Van\u00a0Dinh","family":"Tran","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-9564-7525","authenticated-orcid":false,"given":"Florian","family":"Eggenhofer","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany"}]},{"given":"Shiraz\u00a0A","family":"Shah","sequence":"additional","affiliation":[{"name":"Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Denmark"}]},{"given":"Ekrem","family":"\u00d6zt\u00fcrk","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany"}]},{"given":"Victor\u00a0A","family":"Padilha","sequence":"additional","affiliation":[{"name":"Institute of Mathematics and Computer Sciences, University of S\u00e3o Paulo, S\u00e3o Carlos, SP, Brazil"}]},{"given":"Danilo\u00a0S","family":"Sanches","sequence":"additional","affiliation":[{"name":"Universidade Tecnol\u00f3gica Federal do Paran\u00e1, Campus Corn\u00e9lio Proc\u00f3pio, 86300000 Corn\u00e9lio Proc\u00f3pio, PR,\u00a0Brazil"}]},{"given":"Andr\u00e9\u00a0C\u00a0P\u00a0L\u00a0F","family":"de\u00a0Carvalho","sequence":"additional","affiliation":[{"name":"Institute of Mathematics and Computer Sciences, University of S\u00e3o Paulo, S\u00e3o Carlos, SP, Brazil"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-8231-3323","authenticated-orcid":false,"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany"},{"name":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,6,16]]},"reference":[{"key":"2021070812202369400_B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-3-642-34657-6","volume-title":"CRISPR\u2013Cas Systems: RNA-mediated Adaptive Immunity in Bacteria and Archaea","author":"Barrangou","year":"2013"},{"key":"2021070812202369400_B2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.ymeth.2019.07.013","article-title":"CRISPR\u2013Cas bioinformatics","volume":"172","author":"Alkhnbashi","year":"2020","journal-title":"Methods"},{"key":"2021070812202369400_B3","doi-asserted-by":"crossref","first-page":"8034","DOI":"10.1093\/nar\/gkt606","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":"2021070812202369400_B4","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/nrmicro3569","article-title":"An updated evolutionary classification of CRISPR\u2013Cas systems","volume":"13","author":"Makarova","year":"2015","journal-title":"Nat. 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