{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T22:42:31Z","timestamp":1777934551289,"version":"3.51.4"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,5,27]],"date-time":"2020-05-27T00:00:00Z","timestamp":1590537600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["1092262"],"award-info":[{"award-number":["1092262"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61862017"],"award-info":[{"award-number":["61862017"]}],"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><jats:p>Anti-CRISPRs are widespread amongst bacteriophage and promote bacteriophage infection by inactivating the bacterial host's CRISPR\u2013Cas defence system. Identifying and characterizing anti-CRISPR proteins opens an avenue to explore and control CRISPR\u2013Cas machineries for the development of new CRISPR\u2013Cas based biotechnological and therapeutic tools. Past studies have identified anti-CRISPRs in several model phage genomes, but a challenge exists to comprehensively screen for anti-CRISPRs accurately and efficiently from genome and metagenome sequence data. Here, we have developed an ensemble learning based predictor, PaCRISPR, to accurately identify anti-CRISPRs from protein datasets derived from genome and metagenome sequencing projects. PaCRISPR employs different types of feature recognition united within an ensemble framework. Extensive cross-validation and independent tests show that PaCRISPR achieves a significantly more accurate performance compared with homology-based baseline predictors and an existing toolkit. The performance of PaCRISPR was further validated in discovering anti-CRISPRs that were not part of the training for PaCRISPR, but which were recently demonstrated to function as anti-CRISPRs for phage infections. Data visualization on anti-CRISPR relationships, highlighting sequence similarity and phylogenetic considerations, is part of the output from the PaCRISPR toolkit, which is freely available at http:\/\/pacrispr.erc.monash.edu\/.<\/jats:p>","DOI":"10.1093\/nar\/gkaa432","type":"journal-article","created":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T11:36:42Z","timestamp":1589456202000},"page":"W348-W357","source":"Crossref","is-referenced-by-count":60,"title":["PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins"],"prefix":"10.1093","volume":"48","author":[{"given":"Jiawei","family":"Wang","sequence":"first","affiliation":[{"name":"Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia"}]},{"given":"Wei","family":"Dai","sequence":"first","affiliation":[{"name":"Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia"},{"name":"School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China"}]},{"given":"Jiahui","family":"Li","sequence":"first","affiliation":[{"name":"School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China"}]},{"given":"Ruopeng","family":"Xie","sequence":"first","affiliation":[{"name":"School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China"}]},{"given":"Rhys A","family":"Dunstan","sequence":"first","affiliation":[{"name":"Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia"}]},{"given":"Christopher","family":"Stubenrauch","sequence":"first","affiliation":[{"name":"Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8629-258X","authenticated-orcid":false,"given":"Yanju","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0102-7884","authenticated-orcid":false,"given":"Trevor","family":"Lithgow","sequence":"first","affiliation":[{"name":"Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia"}]}],"member":"286","published-online":{"date-parts":[[2020,5,27]]},"reference":[{"key":"2020062614050556900_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":"2020062614050556900_B2","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":"Annu Rev Virol"},{"key":"2020062614050556900_B3","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.molcel.2017.09.002","article-title":"The anti-CRISPR story: a battle for survival","volume":"68","author":"Maxwell","year":"2017","journal-title":"Mol. 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