{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T18:38:23Z","timestamp":1781980703903,"version":"3.54.5"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T00:00:00Z","timestamp":1684281600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is designed to support the rapid identification, annotation and visualization of prophage sequences within bacterial genomes and plasmids. PHASTEST also supports rapid annotation and interactive visualization of all other genes (protein coding regions, tRNA\/tmRNA\/rRNA sequences) in bacterial genomes. Given that bacterial genome sequencing has become so routine, the need for fast tools to comprehensively annotate bacterial genomes has become progressively more important. PHASTEST not only offers faster and more accurate prophage annotations than its predecessors, it also provides more complete whole genome annotations and much improved genome visualization capabilities. In standardized tests, we found that PHASTEST is 31% faster and 2\u20133% more accurate in prophage identification than PHASTER. Specifically, PHASTEST can process a typical bacterial genome in 3.2 min\u00a0(raw sequence) or in 1.3 min\u00a0when given a pre-annotated GenBank file. Improvements in PHASTEST\u2019s ability to annotate bacterial genomes now make it a particularly powerful tool for whole genome annotation. In addition, PHASTEST now offers a much more modern and responsive visualization interface that allows users to generate, edit, annotate and interactively visualize (via zooming, rotating, dragging, panning, resetting), colourful, publication quality genome maps. PHASTEST continues to offer popular options such as an API for programmatic queries, a Docker image for local installations, support for multiple (metagenomic) queries and the ability to perform automated look-ups against thousands of previously PHAST-annotated bacterial genomes. PHASTEST is available online at https:\/\/phastest.ca.<\/jats:p>","DOI":"10.1093\/nar\/gkad382","type":"journal-article","created":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T10:48:27Z","timestamp":1684320507000},"page":"W443-W450","source":"Crossref","is-referenced-by-count":596,"title":["PHASTEST: faster than PHASTER, better than PHAST"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3207-2434","authenticated-orcid":false,"given":"David S","family":"Wishart","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton , AB ,\u00a0T6G 2E9, Canada"},{"name":"Department of Computing Science, University of Alberta , Edmonton , AB ,\u00a0T6G 2E8, Canada"},{"name":"Department of Laboratory Medicine and Pathology, University of Alberta , Edmonton , AB ,\u00a0T6G 2B7, Canada"},{"name":"Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta , Edmonton , AB ,\u00a0T6G 2H7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton , AB ,\u00a0T6G 2E9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sukanta","family":"Saha","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton , AB ,\u00a0T6G 2E9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eponine","family":"Oler","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton , AB ,\u00a0T6G 2E9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harrison","family":"Peters","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton , AB ,\u00a0T6G 2E9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason\u00a0R","family":"Grant","sequence":"additional","affiliation":[{"name":"Department of Agricultural, Food and Nutritional Science, University of Alberta , Edmonton , AB ,\u00a0T6G 2P5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4263-969X","authenticated-orcid":false,"given":"Paul","family":"Stothard","sequence":"additional","affiliation":[{"name":"Department of Agricultural, Food and Nutritional Science, University of Alberta , Edmonton , AB ,\u00a0T6G 2P5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasuk","family":"Gautam","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton , AB ,\u00a0T6G 2E9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,17]]},"reference":[{"key":"2023070504585429000_B1","doi-asserted-by":"crossref","first-page":"354","DOI":"10.4161\/viru.24498","article-title":"Importance of prophages to evolution and virulence of bacterial pathogens","volume":"4","author":"Fortier","year":"2013","journal-title":"Virulence"},{"key":"2023070504585429000_B2","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1046\/j.1365-2958.2003.03580.x","article-title":"Prophages and bacterial genomics: what have we learned so far?","volume":"49","author":"Casjens","year":"2003","journal-title":"Mol. 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