{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T03:22:53Z","timestamp":1779247373963,"version":"3.51.4"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,5,13]],"date-time":"2020-05-13T00:00:00Z","timestamp":1589328000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1933521"],"award-info":[{"award-number":["DBI-1933521"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"United States Department of Agriculture","doi-asserted-by":"publisher","award":["58\u20138042-9\u2013089"],"award-info":[{"award-number":["58\u20138042-9\u2013089"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008114","name":"UNL","doi-asserted-by":"publisher","award":["2019-YIN"],"award-info":[{"award-number":["2019-YIN"]}],"id":[{"id":"10.13039\/100008114","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31728013"],"award-info":[{"award-number":["31728013"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61973174"],"award-info":[{"award-number":["61973174"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Anti-CRISPR (Acr) proteins encoded by (pro)phages\/(pro)viruses have a great potential to enable a more controllable genome editing. However, genome mining new Acr proteins is challenging due to the lack of a conserved functional domain and the low sequence similarity among experimentally characterized Acr proteins. We introduce here AcrFinder, a web server (http:\/\/bcb.unl.edu\/AcrFinder) that combines three well-accepted ideas used by previous experimental studies to pre-screen genomic data for Acr candidates. These ideas include homology search, guilt-by-association (GBA), and CRISPR-Cas self-targeting spacers. Compared to existing bioinformatics tools, AcrFinder has the following unique functions: (i) it is the first online server specifically mining genomes for Acr-Aca operons; (ii) it provides a most comprehensive Acr and Aca (Acr-associated regulator) database (populated by GBA-based Acr and Aca datasets); (iii) it combines homology-based, GBA-based, and self-targeting approaches in one software package; and (iv) it provides a user-friendly web interface to take both nucleotide and protein sequence files as inputs, and output a result page with graphic representation of the genomic contexts of Acr-Aca operons. The leave-one-out cross-validation on experimentally characterized Acr-Aca operons showed that AcrFinder had a 100% recall. AcrFinder will be a valuable web resource to help experimental microbiologists discover new Anti-CRISPRs.<\/jats:p>","DOI":"10.1093\/nar\/gkaa351","type":"journal-article","created":{"date-parts":[[2020,5,12]],"date-time":"2020-05-12T03:09:45Z","timestamp":1589252985000},"page":"W358-W365","source":"Crossref","is-referenced-by-count":71,"title":["AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses"],"prefix":"10.1093","volume":"48","author":[{"given":"Haidong","family":"Yi","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of North Carolina at Chapel Hill, NC, USA"},{"name":"College of Computer Science, Nankai University, Tianjin, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Le","family":"Huang","sequence":"first","affiliation":[{"name":"College of Computer Science, Nankai University, Tianjin, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bowen","family":"Yang","sequence":"first","affiliation":[{"name":"Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javi","family":"Gomez","sequence":"first","affiliation":[{"name":"Department of Computer Science, Northern Illinois University, DeKalb, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8498-3451","authenticated-orcid":false,"given":"Han","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Artificial Intelligence, Nankai University, Tianjin, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7667-881X","authenticated-orcid":false,"given":"Yanbin","family":"Yin","sequence":"first","affiliation":[{"name":"Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,5,13]]},"reference":[{"key":"2020062614042191200_B1","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1038\/nature11723","article-title":"Bacteriophage genes that inactivate the CRISPR\/Cas bacterial immune system","volume":"493","author":"Bondy-Denomy","year":"2013","journal-title":"Nature"},{"key":"2020062614042191200_B2","doi-asserted-by":"crossref","first-page":"9658","DOI":"10.1093\/nar\/gkz721","article-title":"The autoregulator Aca2 mediates anti-CRISPR repression","volume":"47","author":"Birkholz","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614042191200_B3","doi-asserted-by":"crossref","first-page":"1452","DOI":"10.1016\/j.cell.2019.07.046","article-title":"Anti-CRISPR-Associated proteins are crucial repressors of Anti-CRISPR transcription","volume":"178","author":"Stanley","year":"2019","journal-title":"Cell"},{"key":"2020062614042191200_B4","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1146\/annurev-virology-101416-041616","article-title":"The discovery, mechanisms, and evolutionary impact of Anti-CRISPRs","volume":"4","author":"Borges","year":"2017","journal-title":"Ann. Rev. Virol."},{"key":"2020062614042191200_B5","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1021\/acschembio.7b00831","article-title":"Protein inhibitors of CRISPR-Cas9","volume":"13","author":"Bondy-Denomy","year":"2018","journal-title":"ACS Chem. Biol."},{"key":"2020062614042191200_B6","doi-asserted-by":"crossref","first-page":"1829","DOI":"10.1016\/j.cell.2016.11.017","article-title":"naturally occurring off-switches for CRISPR-Cas9","volume":"167","author":"Pawluk","year":"2016","journal-title":"Cell"},{"key":"2020062614042191200_B7","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1038\/nrmicro.2017.120","article-title":"Anti-CRISPR: discovery, mechanism and function","volume":"16","author":"Pawluk","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"2020062614042191200_B8","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1038\/s41467-018-08158-x","article-title":"Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells","volume":"10","author":"Nakamura","year":"2019","journal-title":"Nat. Commun."},{"key":"2020062614042191200_B9","doi-asserted-by":"crossref","first-page":"e1701620","DOI":"10.1126\/sciadv.1701620","article-title":"Disabling Cas9 by an anti-CRISPR DNA mimic","volume":"3","author":"Shin","year":"2017","journal-title":"Sci. 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Sci."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/W1\/W358\/33433393\/gkaa351.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/W1\/W358\/33433393\/gkaa351.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,27]],"date-time":"2020-06-27T06:30:56Z","timestamp":1593239456000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/W1\/W358\/5836766"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,13]]},"references-count":34,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2020,5,13]]},"published-print":{"date-parts":[[2020,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaa351","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,7,2]]},"published":{"date-parts":[[2020,5,13]]}}}