{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T09:46:07Z","timestamp":1771062367039,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2020,11,23]],"date-time":"2020-11-23T00:00:00Z","timestamp":1606089600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","award":["54308198"],"award-info":[{"award-number":["54308198"]}],"id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","award":["GT12053"],"award-info":[{"award-number":["GT12053"]}],"id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","award":["54308199"],"award-info":[{"award-number":["54308199"]}],"id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Bacteriophages (phages) are incredibly abundant and genetically diverse. The volume of phage genomics data is rapidly increasing, driven in part by the SEA-PHAGES program, which isolates, sequences and manually annotates hundreds of phage genomes each year. With an ever-expanding genomics dataset, there are many opportunities for generating new biological insights through comparative genomic and bioinformatic analyses. As a result, there is a growing need to be able to store, update, explore and analyze phage genomics data. The package pdm_utils provides a collection of tools for MySQL phage database management designed to meet specific needs in the SEA-PHAGES program and phage genomics generally.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/pypi.org\/project\/pdm-utils\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa983","type":"journal-article","created":{"date-parts":[[2020,11,11]],"date-time":"2020-11-11T01:56:59Z","timestamp":1605059819000},"page":"2464-2466","source":"Crossref","is-referenced-by-count":15,"title":["pdm_utils: a SEA-PHAGES MySQL phage database management toolkit"],"prefix":"10.1093","volume":"37","author":[{"given":"Travis N","family":"Mavrich","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Pittsburgh , Pittsburgh, PA 15260, USA"}]},{"given":"Christian","family":"Gauthier","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Pittsburgh , Pittsburgh, PA 15260, USA"}]},{"given":"Lawrence","family":"Abad","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Pittsburgh , Pittsburgh, PA 15260, USA"}]},{"given":"Charles A","family":"Bowman","sequence":"additional","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, CA 92037, USA"}]},{"given":"Steven G","family":"Cresawn","sequence":"additional","affiliation":[{"name":"Department of Biology, James Madison University , Harrisonburg, VA 22807, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6705-6821","authenticated-orcid":false,"given":"Graham F","family":"Hatfull","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Pittsburgh , Pittsburgh, PA 15260, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,11,23]]},"reference":[{"key":"2023051609060580600_btaa983-B1","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023051609060580600_btaa983-B2","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1146\/annurev-virology-100114-054952","article-title":"Viruses as winners in the game of life","volume":"3","author":"Cobian Guemes","year":"2016","journal-title":"Annu. 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