{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T07:59:59Z","timestamp":1775807999478,"version":"3.50.1"},"reference-count":94,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T00:00:00Z","timestamp":1653436800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Royal Society of New Zealand Te Ap\u0101rangi (RSNZ) Marsden"},{"DOI":"10.13039\/100008247","name":"University of Otago","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008247","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Bioprotection Aotearoa"},{"name":"University of Otago Doctoral Scholarship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Most bacteria and archaea possess multiple antiviral defence systems that protect against infection by phages, archaeal viruses and mobile genetic elements. Our understanding of the diversity of defence systems has increased greatly in the last few years, and many more systems likely await discovery. To identify defence-related genes, we recently developed the Prokaryotic Antiviral Defence LOCator (PADLOC) bioinformatics tool. To increase the accessibility of PADLOC, we describe here the PADLOC web server (freely available at https:\/\/padloc.otago.ac.nz), allowing users to analyse whole genomes, metagenomic contigs, plasmids, phages and archaeal viruses. The web server includes a more than 5-fold increase in defence system types detected (since the first release) and expanded functionality enabling detection of CRISPR arrays and retron ncRNAs. Here, we provide user information such as input options, description of the multiple outputs, limitations and considerations for interpretation of the results, and guidance for subsequent analyses. The PADLOC web server also houses a precomputed database of the defence systems in\u00a0&amp;gt;\u00a0230,000 RefSeq genomes. These data reveal two taxa, Campylobacterota and Spriochaetota, with unusual defence system diversity and abundance. Overall, the PADLOC web server provides a convenient and accessible resource for the detection of antiviral defence systems.<\/jats:p>","DOI":"10.1093\/nar\/gkac400","type":"journal-article","created":{"date-parts":[[2022,5,6]],"date-time":"2022-05-06T11:36:33Z","timestamp":1651836993000},"page":"W541-W550","source":"Crossref","is-referenced-by-count":215,"title":["PADLOC: a web server for the identification of antiviral defence systems in microbial genomes"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2305-6827","authenticated-orcid":false,"given":"Leighton J","family":"Payne","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, University of Otago , Dunedin , New Zealand"}]},{"given":"Sean","family":"Meaden","sequence":"additional","affiliation":[{"name":"Biosciences, University of Exeter , Penryn , UK"}]},{"given":"Mario R","family":"Mestre","sequence":"additional","affiliation":[{"name":"Independent Researcher , Spain"}]},{"given":"Chris","family":"Palmer","sequence":"additional","affiliation":[{"name":"Information Technology Services Research and Teaching Group, University of Otago , Dunedin , New Zealand"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3614-807X","authenticated-orcid":false,"given":"Nicol\u00e1s","family":"Toro","sequence":"additional","affiliation":[{"name":"Department of Soil Microbiology and Symbiotic Systems, Estaci\u00f3n Experimental del Zaid\u00edn, Consejo Superior de Investigaciones Cient\u00edficas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecolog\u00eda Gen\u00e9tica de la Rizosfera , Granada , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4639-6704","authenticated-orcid":false,"given":"Peter\u00a0C","family":"Fineran","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Otago , Dunedin , New Zealand"},{"name":"Genetics Otago, University of Otago , Dunedin , New Zealand"},{"name":"Bioprotection Aotearoa, University of Otago , Dunedin , New Zealand"},{"name":"Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago , Dunedin , New Zealand"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4512-3093","authenticated-orcid":false,"given":"Simon\u00a0A","family":"Jackson","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Otago , Dunedin , New Zealand"},{"name":"Genetics Otago, University of Otago , Dunedin , New Zealand"},{"name":"Bioprotection Aotearoa, University of Otago , Dunedin , New Zealand"},{"name":"Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago , Dunedin , New Zealand"}]}],"member":"286","published-online":{"date-parts":[[2022,5,25]]},"reference":[{"key":"2022070500010390600_B1","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/s41579-019-0278-2","article-title":"The pan-immune system of bacteria: antiviral defence as a community resource","volume":"18","author":"Bernheim","year":"2020","journal-title":"Nat. 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