{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T15:18:04Z","timestamp":1791559084603,"version":"4.3.4"},"reference-count":28,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"vor","delay-in-days":6,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Protocols"],"published-print":{"date-parts":[[2026,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Viral metagenomics is an increasingly powerful tool for understanding the function and structure of viruses across the diverse environments of our planet. However, decoding the functional potential of prokaryotic viral metagenomes is extremely challenging. Pharokka, Phold, and Phynteny are complementary open\u2010source prokaryotic viral genome annotation tools that utilize a variety of bioinformatics approaches to maximally annotate viral metagenomes. This article describes a protocol for installing and running these tools on a viral metagenomic dataset, followed by visualization of annotations using our client\u2010side Phold Plot web assembly application. \u00a9 2026 The Author(s).\n                    <jats:italic>Current Protocols<\/jats:italic>\n                    published by Wiley Periodicals LLC.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 1<\/jats:bold>\n                    : Prokaryotic viral metagenome annotation with Pharokka\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 2<\/jats:bold>\n                    : Enhanced prokaryotic viral metagenome protein annotation using protein structures with Phold\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 3<\/jats:bold>\n                    : Further prokaryotic viral metagenome protein annotation using genome synteny and protein language models with Phynteny\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 4<\/jats:bold>\n                    : Visualization of prokaryotic viral metagenome annotations with Phold Plot web assembly application\n                  <\/jats:p>","DOI":"10.1002\/cpz1.70405","type":"journal-article","created":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T10:27:24Z","timestamp":1783420044000},"source":"Crossref","is-referenced-by-count":1,"title":["Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny"],"prefix":"10.1002","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5885-4186","authenticated-orcid":false,"given":"George","family":"Bouras","sequence":"first","affiliation":[{"name":"School of Medicine, College of Health Adelaide University  Adelaide Australia"},{"name":"The Department of Surgery \u2013 Otolaryngology Head and Neck Surgery Central Adelaide Local Health Network  Adelaide Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanna R.","family":"Grigson","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute Lawrence Berkeley National Laboratory  Berkeley California"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lindsay","family":"Durr","sequence":"additional","affiliation":[{"name":"School of Medicine, College of Health Adelaide University  Adelaide Australia"},{"name":"The Department of Surgery \u2013 Otolaryngology Head and Neck Surgery Central Adelaide Local Health Network  Adelaide Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bhavya","family":"Papudeshi","sequence":"additional","affiliation":[{"name":"Department of Fundamental Microbiology University of Lausanne  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vijini","family":"Mallawaarachchi","sequence":"additional","affiliation":[{"name":"Flinders Accelerator for Microbiome Exploration, College of Science and Engineering Flinders University  Bedford Park Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4719-9785","authenticated-orcid":false,"given":"Sarah","family":"Vreugde","sequence":"additional","affiliation":[{"name":"School of Medicine, College of Health Adelaide University  Adelaide Australia"},{"name":"The Department of Surgery \u2013 Otolaryngology Head and Neck Surgery Central Adelaide Local Health Network  Adelaide Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8383-8949","authenticated-orcid":false,"given":"Robert A.","family":"Edwards","sequence":"additional","affiliation":[{"name":"Flinders Accelerator for Microbiome Exploration, 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