{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T18:00:53Z","timestamp":1775239253310,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,7,30]],"date-time":"2019-07-30T00:00:00Z","timestamp":1564444800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Portuguese Foundation for Science and Technology"},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["UID\/BIO\/04469\/2019"],"award-info":[{"award-number":["UID\/BIO\/04469\/2019"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["POCI-01-0145-FEDER-029628"],"award-info":[{"award-number":["POCI-01-0145-FEDER-029628"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["NORTE-01-0145-FEDER-000004"],"award-info":[{"award-number":["NORTE-01-0145-FEDER-000004"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The growing interest in phages as antibacterial agents has led to an increase in the number of sequenced phage genomes, increasing the need for intuitive bioinformatics tools for performing genome annotation. The identification of phage promoters is indeed the most difficult step of this process. Due to the lack of online tools for phage promoter prediction, we developed PhagePromoter, a tool for locating promoters in phage genomes, using machine learning methods. This is the first online tool for predicting promoters that uses phage promoter data and the first to identify both host and phage promoters with different motifs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>This tool was integrated in the Galaxy framework and it is available online at: https:\/\/bit.ly\/2Dfebfv.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz580","type":"journal-article","created":{"date-parts":[[2019,7,24]],"date-time":"2019-07-24T19:17:27Z","timestamp":1563995847000},"page":"5301-5302","source":"Crossref","is-referenced-by-count":62,"title":["Predicting promoters in phage genomes using <i>PhagePromoter<\/i>"],"prefix":"10.1093","volume":"35","author":[{"given":"Marta","family":"Sampaio","sequence":"first","affiliation":[{"name":"Centre of Biological Engineering, School of Engineering, University of Minho , Braga, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8439-8172","authenticated-orcid":false,"given":"Miguel","family":"Rocha","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, School of Engineering, University of Minho , Braga, Portugal"}]},{"given":"Hugo","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, School of Engineering, University of Minho , Braga, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1765-7178","authenticated-orcid":false,"given":"Oscar","family":"Dias","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, School of Engineering, University of Minho , Braga, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2019,7,29]]},"reference":[{"key":"2023020108351724300_btz580-B1","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: tools for motif discovery and searching","volume":"37","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023020108351724300_btz580-B2","doi-asserted-by":"crossref","first-page":"e1062588.","DOI":"10.1080\/21597081.2015.1062588","article-title":"Bioinformatics as a first-line approach for understanding bacteriophage transcription","volume":"5","author":"Guzina","year":"2015","journal-title":"Bacteriophage"},{"key":"2023020108351724300_btz580-B3","doi-asserted-by":"crossref","first-page":"9.","DOI":"10.1186\/1743-422X-9-9","article-title":"Bacteriophages and their implications on future biotechnology: a review","volume":"9","author":"Haq","year":"2012","journal-title":"Virol. 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