{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T07:50:34Z","timestamp":1772524234987,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,3,6]],"date-time":"2023-03-06T00:00:00Z","timestamp":1678060800000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFA0908700"],"award-info":[{"award-number":["2020YFA0908700"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62072003"],"award-info":[{"award-number":["62072003"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62272004"],"award-info":[{"award-number":["62272004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11835014"],"award-info":[{"award-number":["11835014"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U19A2064"],"award-info":[{"award-number":["U19A2064"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Education Department of Anhui Province","award":["KJ2020A0047"],"award-info":[{"award-number":["KJ2020A0047"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes. Accordingly, comprehensive and user-friendly platforms for phage genome annotation are needed.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we propose PhaGAA, an online integrated platform for phage genome annotation and analysis. By incorporating several annotation tools, PhaGAA is constructed to annotate the prophage genome at DNA and protein levels and provide the analytical results. Furthermore, PhaGAA could mine and annotate phage genomes from bacterial genome or metagenome. In summary, PhaGAA will be a useful resource for experimental biologists and help advance the phage synthetic biology in basic and application research.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>PhaGAA is freely available at http:\/\/phage.xialab.info\/.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad120","type":"journal-article","created":{"date-parts":[[2023,3,8]],"date-time":"2023-03-08T00:53:55Z","timestamp":1678236835000},"source":"Crossref","is-referenced-by-count":16,"title":["PhaGAA: an integrated web server platform for phage genome annotation and analysis"],"prefix":"10.1093","volume":"39","author":[{"given":"Jiawei","family":"Wu","sequence":"first","affiliation":[{"name":"Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, and Institutes of Physical Science and Information Technology, Anhui University , Hefei, Anhui 230601, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingrui","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, and Institutes of Physical Science and Information Technology, Anhui University , Hefei, Anhui 230601, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Min","family":"Li","sequence":"additional","affiliation":[{"name":"BGI-Shenzhen, Shenzhen 518083, China"},{"name":"Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen , Shenzhen 518083, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiliang","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Anhui University , Hefei, Anhui 230601, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, and Institutes of Physical Science and Information Technology, Anhui University , Hefei, Anhui 230601, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junyin","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Anhui University , Hefei, Anhui 230601, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minfeng","family":"Xiao","sequence":"additional","affiliation":[{"name":"BGI-Shenzhen, Shenzhen 518083, China"},{"name":"Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen , Shenzhen 518083, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6122-5930","authenticated-orcid":false,"given":"Yannan","family":"Bin","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, and Institutes of Physical Science and Information Technology, Anhui University , Hefei, Anhui 230601, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3024-1705","authenticated-orcid":false,"given":"Junfeng","family":"Xia","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, and Institutes of Physical Science and Information Technology, Anhui University , Hefei, Anhui 230601, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,3,6]]},"reference":[{"key":"2023031415582595100_","author":"Amgarten","year":"2020"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"e121","DOI":"10.1093\/nar\/gkaa856","article-title":"Seeker: alignment-free identification of bacteriophage genomes by deep learning","volume":"48","author":"Auslander","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.1093\/nar\/29.12.2607","article-title":"GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions","volume":"29","author":"Besemer","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"e1007845","DOI":"10.1371\/journal.pcbi.1007845","article-title":"PhANNs, a fast and accurate tool and web server to classify phage structural proteins","volume":"16","author":"Cantu","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1007\/s10822-020-00323-z","article-title":"Meta-iPVP: a sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation","volume":"34","author":"Charoenkwan","year":"2020","journal-title":"J Comput Aided Mol Des"},{"key":"2023031415582595100_","author":"Coutinho","year":"2020"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"4636","DOI":"10.1093\/nar\/27.23.4636","article-title":"Improved microbial gene identification with GLIMMER","volume":"27","author":"Delcher","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giz066","article-title":"PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning","volume":"8","author":"Fang","year":"2019","journal-title":"Gigascience"},{"key":"2023031415582595100_","first-page":"885048","article-title":"DBSCAN-SWA: an integrated tool for rapid prophage detection and annotation","volume-title":"Frontiers in Genetics","author":"Gan","year":"2022"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"e11396","DOI":"10.7717\/peerj.11396","article-title":"BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains","volume":"9","author":"Hockenberry","year":"2021","journal-title":"PeerJ"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/j.drudis.2009.03.006","article-title":"Phage therapy","volume":"14","author":"Housby","year":"2009","journal-title":"Drug Discov Today"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinform"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat Commun"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1007\/s12275-021-1154-0","article-title":"Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity","volume":"59","author":"Kim","year":"2021","journal-title":"J Microbiol"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1186\/s12859-018-2342-8","article-title":"Phage spanins: diversity, topological dynamics and gene convergence","volume":"19","author":"Kongari","year":"2018","journal-title":"BMC Bioinform"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"4537","DOI":"10.1093\/bioinformatics\/btz265","article-title":"PHANOTATE: a novel approach to gene identification in phage genomes","volume":"35","author":"McNair","year":"2019","journal-title":"Bioinformatics"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","article-title":"CheckV assesses the quality and completeness of metagenome-assembled viral genomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2023031415582595100_","first-page":"D535","article-title":"CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and CAS genes from complete genome sequences, and tools to download and query lists of repeats and spacers","volume":"48","author":"Pourcel","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"e1008214","DOI":"10.1371\/journal.pcbi.1008214","article-title":"Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation","volume":"16","author":"Ramsey","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"5301","DOI":"10.1093\/bioinformatics\/btz580","article-title":"Predicting promoters in phage genomes using PhagePromoter","volume":"35","author":"Sampaio","year":"2019","journal-title":"Bioinformatics"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"2023031415582595100_","author":"Shang","year":"2022"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"lqaa109","DOI":"10.1093\/nargab\/lqaa109","article-title":"Rapid discovery of novel prophages using biological feature engineering and machine learning","volume":"3","author":"Siren","year":"2021","journal-title":"NAR Genom. Bioinform"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"W74","DOI":"10.1093\/nar\/gkz380","article-title":"Prophage hunter: an integrative hunting tool for active prophages","volume":"47","author":"Song","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"3882","DOI":"10.1093\/bioinformatics\/btaa250","article-title":"Phigaro: high-throughput prophage sequence annotation","volume":"36","author":"Starikova","year":"2020","journal-title":"Bioinformatics"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"lqab067","DOI":"10.1093\/nargab\/lqab067","article-title":"PHROG: families of prokaryotic virus proteins clustered using remote homology","volume":"3","author":"Terzian","year":"2021","journal-title":"NAR Genom Bioinform"},{"key":"2023031415582595100_","author":"Tynecki","year":"2020"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"5258","DOI":"10.1109\/JBHI.2022.3193224","article-title":"DPProm: a two-layer predictor for identifying promoters and their types on phage genome using deep learning","volume":"26","author":"Wang","year":"2022","journal-title":"IEEE J Biomed Health Inform"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"lqaa044","DOI":"10.1093\/nargab\/lqaa044","article-title":"A network-based integrated framework for predicting virus-prokaryote interactions","volume":"2","author":"Wang","year":"2020","journal-title":"NAR Genom Bioinform"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"giab056","DOI":"10.1093\/gigascience\/giab056","article-title":"DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach","volume":"10","author":"Wu","year":"2021","journal-title":"Gigascience"},{"key":"2023031415582595100_","doi-asserted-by":"crossref","first-page":"W6","DOI":"10.1093\/nar\/gkl164","article-title":"BLAST: improvements for better sequence analysis","volume":"34","author":"Ye","year":"2006","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad120\/49434203\/btad120.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/3\/btad120\/49523754\/btad120.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/3\/btad120\/49523754\/btad120.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,27]],"date-time":"2023-03-27T13:23:28Z","timestamp":1679923408000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad120\/7070502"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,3,1]]},"references-count":32,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad120","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,3,1]]},"published":{"date-parts":[[2023,3,1]]},"article-number":"btad120"}}