{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T06:53:05Z","timestamp":1774507985155,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008214","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,11,12]],"date-time":"2020-11-12T00:00:00Z","timestamp":1605139200000}}],"reference-count":76,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2020,11,2]],"date-time":"2020-11-02T00:00:00Z","timestamp":1604275200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["EF-0949351"],"award-info":[{"award-number":["EF-0949351"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1565146"],"award-info":[{"award-number":["DBI-1565146"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1565146"],"award-info":[{"award-number":["DBI-1565146"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1565146"],"award-info":[{"award-number":["DBI-1565146"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>In the modern genomic era, scientists without extensive bioinformatic training need to apply high-power computational analyses to critical tasks like phage genome annotation. At the Center for Phage Technology (CPT), we developed a suite of phage-oriented tools housed in open, user-friendly web-based interfaces. A Galaxy platform conducts computationally intensive analyses and Apollo, a collaborative genome annotation editor, visualizes the results of these analyses. The collection includes open source applications such as the BLAST+ suite, InterProScan, and several gene callers, as well as unique tools developed at the CPT that allow maximum user flexibility. We describe in detail programs for finding Shine-Dalgarno sequences, resources used for confident identification of lysis genes such as spanins, and methods used for identifying interrupted genes that contain frameshifts or introns. At the CPT, genome annotation is separated into two robust segments that are facilitated through the automated execution of many tools chained together in an operation called a workflow. First, the structural annotation workflow results in gene and other feature calls. This is followed by a functional annotation workflow that combines sequence comparisons and conserved domain searching, which is contextualized to allow integrated evidence assessment in functional prediction. Finally, we describe a workflow used for comparative genomics. Using this multi-purpose platform enables researchers to easily and accurately annotate an entire phage genome. The portal can be accessed at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/cpt.tamu.edu\/galaxy-pub\" xlink:type=\"simple\">https:\/\/cpt.tamu.edu\/galaxy-pub<\/jats:ext-link> with accompanying user training material.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008214","type":"journal-article","created":{"date-parts":[[2020,11,2]],"date-time":"2020-11-02T18:48:13Z","timestamp":1604342893000},"page":"e1008214","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":139,"title":["Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3774-5896","authenticated-orcid":true,"given":"Jolene","family":"Ramsey","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9760-8992","authenticated-orcid":true,"given":"Helena","family":"Rasche","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0425-0544","authenticated-orcid":true,"given":"Cory","family":"Maughmer","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3835-7625","authenticated-orcid":true,"given":"Anthony","family":"Criscione","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6500-1616","authenticated-orcid":true,"given":"Eleni","family":"Mijalis","sequence":"additional","affiliation":[]},{"given":"Mei","family":"Liu","sequence":"additional","affiliation":[]},{"given":"James C.","family":"Hu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8001-2914","authenticated-orcid":true,"given":"Ry","family":"Young","sequence":"additional","affiliation":[]},{"given":"Jason J.","family":"Gill","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,11,2]]},"reference":[{"key":"pcbi.1008214.ref001","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1016\/j.cell.2017.10.045","article-title":"Contemporary Phage Biology: From Classic Models to New Insights","volume":"172","author":"G Ofir","year":"2018","journal-title":"Cell"},{"key":"pcbi.1008214.ref002","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1038\/nrmicro3564","article-title":"A century of the phage: past, present and future","volume":"13","author":"GPC Salmond","year":"2015","journal-title":"Nat Rev Microbiol"},{"key":"pcbi.1008214.ref003","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1126\/science.aad6791","article-title":"MICROBIOLOGY. Phage therapy redux\u2014What is to be done?","volume":"350","author":"R Young","year":"2015","journal-title":"Science (New York, NY)"},{"key":"pcbi.1008214.ref004","doi-asserted-by":"crossref","first-page":"64","DOI":"10.3390\/v10020064","article-title":"The Magistral Phage","volume":"10","author":"J-P Pirnay","year":"2018","journal-title":"Viruses"},{"key":"pcbi.1008214.ref005","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1089\/bsp.2009.0057","article-title":"Genetically engineered virulent phage banks in the detection and control of emergent pathogenic bacteria","volume":"8","author":"F Pouillot","year":"2010","journal-title":"Biosecurity Bioterrorism Biodefense Strategy Pract Sci"},{"key":"pcbi.1008214.ref006","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/j.coviro.2011.06.009","article-title":"Bacteriophages and their genomes","volume":"1","author":"GF Hatfull","year":"2011","journal-title":"Current opinion in virology"},{"key":"pcbi.1008214.ref007","doi-asserted-by":"crossref","first-page":"D571","DOI":"10.1093\/nar\/gku1207","article-title":"NCBI viral genomes resource","volume":"43","author":"JR Brister","year":"2015","journal-title":"Nucleic acids research"},{"key":"pcbi.1008214.ref008","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s12859-019-2606-y","article-title":"VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank","volume":"20","author":"RC Shean","year":"2019","journal-title":"BMC bioinformatics"},{"key":"pcbi.1008214.ref009","article-title":"multiPhATE: bioinformatics pipeline for functional annotation of phage isolates","author":"CLE Zhou","year":"2019","journal-title":"Bioinformatics"},{"key":"pcbi.1008214.ref010","doi-asserted-by":"crossref","first-page":"188","DOI":"10.3390\/v10040188","article-title":"Characterizing Phage Genomes for Therapeutic Applications","volume":"10","author":"C Philipson","year":"2018","journal-title":"Viruses"},{"key":"pcbi.1008214.ref011","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"E Afgan","year":"2018","journal-title":"Nucleic acids research"},{"key":"pcbi.1008214.ref012","doi-asserted-by":"crossref","first-page":"R93","DOI":"10.1186\/gb-2013-14-8-r93","article-title":"Web Apollo: a web-based genomic annotation editing platform","volume":"14","author":"E Lee","year":"2013","journal-title":"Genome biology"},{"key":"pcbi.1008214.ref013","doi-asserted-by":"crossref","first-page":"e1006790","DOI":"10.1371\/journal.pcbi.1006790","article-title":"Apollo: Democratizing genome annotation","volume":"15","author":"NA Dunn","year":"2019","journal-title":"Plos Comput Biol"},{"key":"pcbi.1008214.ref014","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1101\/gr.094607.109","article-title":"JBrowse: a next-generation genome browser","volume":"19","author":"ME Skinner","year":"2009","journal-title":"Genome Res"},{"key":"pcbi.1008214.ref015","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1186\/gb4161","article-title":"Dissemination of scientific software with Galaxy ToolShed","volume":"15","author":"D Blankenberg","year":"2014","journal-title":"Genome Biol"},{"key":"pcbi.1008214.ref016","doi-asserted-by":"crossref","first-page":"e167","DOI":"10.7717\/peerj.167","article-title":"Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology","volume":"1","author":"PJA Cock","year":"2013","journal-title":"Peerj"},{"key":"pcbi.1008214.ref017","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"PJA Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"pcbi.1008214.ref018","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"Consortium U","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008214.ref019","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13059-016-0924-1","article-title":"JBrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"R Buels","year":"2016","journal-title":"Genome Biol"},{"key":"pcbi.1008214.ref020","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1016\/j.cels.2018.05.012","article-title":"Community-Driven Data Analysis Training for Biology","volume":"6","author":"B Batut","year":"2018","journal-title":"Cell Syst"},{"key":"pcbi.1008214.ref021","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.jbi.2010.03.002","article-title":"Evolution of the Sequence Ontology terms and relationships","volume":"44","author":"CJ Mungall","year":"2011","journal-title":"J Biomed Inform"},{"key":"pcbi.1008214.ref022","doi-asserted-by":"crossref","first-page":"R44","DOI":"10.1186\/gb-2005-6-5-r44","article-title":"The Sequence Ontology: a tool for the unification of genome annotations","volume":"6","author":"K Eilbeck","year":"2005","journal-title":"Genome Biol"},{"key":"pcbi.1008214.ref023","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":"R Kongari","year":"2018","journal-title":"BMC bioinformatics"},{"key":"pcbi.1008214.ref024","doi-asserted-by":"crossref","first-page":"2761","DOI":"10.1128\/JB.188.8.2761-2773.2006","article-title":"A Database of Bacterial Lipoproteins (DOLOP) with Functional Assignments to Predicted Lipoproteins","volume":"188","author":"MM Babu","year":"2006","journal-title":"J Bacteriol"},{"key":"pcbi.1008214.ref025","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1093\/protein\/2.7.531","article-title":"The structure of signal peptides from bacterial lipoproteins","volume":"2","author":"G von Heijne","year":"1989","journal-title":"Protein Eng Des Sel"},{"key":"pcbi.1008214.ref026","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/bs.aivir.2018.09.003","article-title":"Phage Lysis: Multiple Genes for Multiple Barriers","volume":"103","author":"J Cahill","year":"2018","journal-title":"Adv Virus Res"},{"key":"pcbi.1008214.ref027","doi-asserted-by":"crossref","first-page":"1652","DOI":"10.1110\/ps.0303703","article-title":"Prediction of lipoprotein signal peptides in Gram-negative bacteria","volume":"12","author":"AS Juncker","year":"2003","journal-title":"Protein science: a publication of the Protein Society"},{"key":"pcbi.1008214.ref028","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes","volume":"305","author":"A Krogh","year":"2001","journal-title":"Journal of Molecular Biology"},{"key":"pcbi.1008214.ref029","first-page":"a003616","article-title":"Group II introns: mobile ribozymes that invade DNA","volume":"3","author":"AM Lambowitz","year":"2011","journal-title":"Csh Perspect Biol"},{"key":"pcbi.1008214.ref030","doi-asserted-by":"crossref","first-page":"D187","DOI":"10.1093\/nar\/gkr1043","article-title":"Database for bacterial group II introns","volume":"40","author":"MA Candales","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008214.ref031","doi-asserted-by":"crossref","first-page":"115","DOI":"10.4161\/mge.20352","article-title":"Cargo capacity of phages and plasmids and other factors influencing horizontal transfers of prokaryote transposable elements","volume":"2","author":"S Leclercq","year":"2012","journal-title":"Mob Genetic Elements"},{"key":"pcbi.1008214.ref032","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1186\/1743-422X-7-290","article-title":"Mobile DNA elements in T4 and related phages","volume":"7","author":"DR Edgell","year":"2010","journal-title":"Virol J"},{"key":"pcbi.1008214.ref033","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.jmb.2006.05.071","article-title":"Plasticity of the Gene Functions for DNA Replication in the T4-like Phages","volume":"361","author":"VM Petrov","year":"2006","journal-title":"J Mol Biol"},{"key":"pcbi.1008214.ref034","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1016\/j.jmb.2009.10.054","article-title":"Genetic Insertions and Diversification of the PolB-Type DNA Polymerase (gp43) of T4-Related Phages","volume":"395","author":"VM Petrov","year":"2010","journal-title":"J Mol Biol"},{"key":"pcbi.1008214.ref035","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/j.tig.2006.01.005","article-title":"Recoding in bacteriophages and bacterial IS elements","volume":"22","author":"PV Baranov","year":"2006","journal-title":"Trends Genet"},{"key":"pcbi.1008214.ref036","first-page":"7007","article-title":"Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use","volume":"44","author":"JF Atkins","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008214.ref037","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.molcel.2004.09.006","article-title":"Conserved translational frameshift in dsDNA bacteriophage tail assembly genes","volume":"16","author":"J Xu","year":"2004","journal-title":"Molecular cell"},{"key":"pcbi.1008214.ref038","doi-asserted-by":"crossref","first-page":"1714","DOI":"10.1128\/JB.186.6.1714-1719.2004","article-title":"A -1 Ribosomal Frameshift in the Transcript That Encodes the Major Head Protein of Bacteriophage A2 Mediates Biosynthesis of a Second Essential Component of the Capsid","volume":"186","author":"P Garcia","year":"2004","journal-title":"J Bacteriol"},{"key":"pcbi.1008214.ref039","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1111\/j.1365-2958.2008.06435.x","article-title":"Origin and function of the two major tail proteins of bacteriophage SPP1","volume":"70","author":"I Auzat","year":"2008","journal-title":"Molecular Microbiology"},{"key":"pcbi.1008214.ref040","doi-asserted-by":"crossref","first-page":"6998","DOI":"10.1128\/JB.173.21.6998-7003.1991","article-title":"Frameshifting in gene 10 of bacteriophage T7","volume":"173","author":"BG Condron","year":"1991","journal-title":"J Bacteriol"},{"key":"pcbi.1008214.ref041","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC bioinformatics"},{"key":"pcbi.1008214.ref042","doi-asserted-by":"crossref","first-page":"8111","DOI":"10.1128\/JVI.03003-14","article-title":"Innovations in Undergraduate Science Education: Going Viral","volume":"89","author":"GF Hatfull","year":"2015","journal-title":"J Virol"},{"key":"pcbi.1008214.ref043","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1186\/s12864-016-3018-2","article-title":"Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies","volume":"17","author":"BD Merrill","year":"2016","journal-title":"BMC genomics"},{"key":"pcbi.1008214.ref044","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"NA O\u2019Leary","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008214.ref045","article-title":"TaxonKit: a cross-platform and efficient NCBI taxonomy toolkit","author":"W Shen","year":"2019","journal-title":"Biorxiv"},{"key":"pcbi.1008214.ref046","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/s41579-019-0311-5","article-title":"Phage diversity, genomics and phylogeny","volume":"18","author":"MB Dion","year":"2020","journal-title":"Nat Rev Microbiol"},{"key":"pcbi.1008214.ref047","doi-asserted-by":"crossref","first-page":"8292","DOI":"10.1038\/s41598-017-07910-5","article-title":"PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data","volume":"7","author":"JR Garneau","year":"2017","journal-title":"Scientific reports"},{"key":"pcbi.1008214.ref048","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":"AL Delcher","year":"1999","journal-title":"Nucleic acids research"},{"key":"pcbi.1008214.ref049","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1093\/dnares\/dsn027","article-title":"MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes","volume":"15","author":"H Noguchi","year":"2008","journal-title":"DNA research: an international journal for rapid publication of reports on genes and genomes"},{"key":"pcbi.1008214.ref050","doi-asserted-by":"crossref","first-page":"R22","DOI":"10.1186\/gb-2007-8-2-r22","article-title":"Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake","volume":"8","author":"CL Kingsford","year":"2007","journal-title":"Genome biology"},{"key":"pcbi.1008214.ref051","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/nar\/gkh152","article-title":"ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences","volume":"32","author":"D Laslett","year":"2004","journal-title":"Nucleic acids research"},{"key":"pcbi.1008214.ref052","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1128\/MMBR.67.1.86-156.2003","article-title":"Bacteriophage T4 Genome","volume":"67","author":"ES Miller","year":"2003","journal-title":"Microbiol Mol Biol R"},{"key":"pcbi.1008214.ref053","first-page":"114819","article-title":"Prophage genomics reveals patterns in phage genome organization and replication","author":"HS Kang","year":"2017","journal-title":"Biorxiv"},{"key":"pcbi.1008214.ref054","article-title":"PHANOTATE: A novel approach to gene identification in phage genomes","author":"K McNair","year":"2019","journal-title":"Bioinformatics"},{"key":"pcbi.1008214.ref055","doi-asserted-by":"crossref","first-page":"e126","DOI":"10.1093\/nar\/gks406","article-title":"PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies","volume":"40","author":"S Akhter","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008214.ref056","doi-asserted-by":"crossref","first-page":"W116","DOI":"10.1093\/nar\/gki442","article-title":"InterProScan: protein domains identifier","volume":"33","author":"E Quevillon","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008214.ref057","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1093\/bioinformatics\/17.9.847","article-title":"InterProScan\u2014an integration platform for the signature-recognition methods in InterPro","volume":"17","author":"EM Zdobnov","year":"2001","journal-title":"Bioinformatics"},{"key":"pcbi.1008214.ref058","doi-asserted-by":"crossref","first-page":"D211","DOI":"10.1093\/nar\/gkn785","article-title":"InterPro: the integrative protein signature database","volume":"37","author":"S Hunter","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008214.ref059","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"P Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"pcbi.1008214.ref060","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1093\/bioinformatics\/btq351","article-title":"BigWig and BigBed: enabling browsing of large distributed datasets","volume":"26","author":"WJ Kent","year":"2010","journal-title":"Bioinformatics"},{"key":"pcbi.1008214.ref061","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1016\/j.jmb.2004.03.016","article-title":"A combined transmembrane topology and signal peptide prediction method","volume":"338","author":"L K\u00e4ll","year":"2004","journal-title":"J Mol Biol"},{"key":"pcbi.1008214.ref062","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/bioinformatics\/btm039","article-title":"Gepard: a rapid and sensitive tool for creating dotplots on genome scale","volume":"23","author":"J Krumsiek","year":"2007","journal-title":"Bioinformatics"},{"key":"pcbi.1008214.ref063","doi-asserted-by":"crossref","first-page":"e11147","DOI":"10.1371\/journal.pone.0011147","article-title":"progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"AE Darling","year":"2010","journal-title":"PloS one"},{"key":"pcbi.1008214.ref064","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btr039","article-title":"Easyfig: a genome comparison visualizer","volume":"27","author":"MJ Sullivan","year":"2011","journal-title":"Bioinform Oxf Engl"},{"key":"pcbi.1008214.ref065","doi-asserted-by":"crossref","first-page":"D393","DOI":"10.1093\/nar\/gkx835","article-title":"Anti-CRISPRdb: a comprehensive online resource for anti-CRISPR proteins","volume":"46","author":"C Dong","year":"2018","journal-title":"Nucleic acids research"},{"key":"pcbi.1008214.ref066","doi-asserted-by":"crossref","first-page":"e01051","DOI":"10.1128\/mBio.01051-13","article-title":"A broadly implementable research course in phage discovery and genomics for first-year undergraduate students","volume":"5","author":"TC Jordan","year":"2014","journal-title":"mBio"},{"key":"pcbi.1008214.ref067","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"T Tatusova","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008214.ref068","doi-asserted-by":"crossref","first-page":"D851","DOI":"10.1093\/nar\/gkx1068","article-title":"RefSeq: an update on prokaryotic genome annotation and curation","volume":"46","author":"DH Haft","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008214.ref069","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1093\/bioinformatics\/btx713","article-title":"DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication","volume":"34","author":"Y Tanizawa","year":"2018","journal-title":"Bioinformatics"},{"key":"pcbi.1008214.ref070","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology","volume":"9","author":"RK Aziz","year":"2008","journal-title":"Bmc Genomics"},{"key":"pcbi.1008214.ref071","doi-asserted-by":"crossref","first-page":"D206","DOI":"10.1093\/nar\/gkt1226","article-title":"The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)","volume":"42","author":"R Overbeek","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008214.ref072","doi-asserted-by":"crossref","first-page":"8365","DOI":"10.1038\/srep08365","article-title":"RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"T Brettin","year":"2015","journal-title":"Sci Rep-uk"},{"key":"pcbi.1008214.ref073","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/978-1-4939-7343-9_17","article-title":"Phage Genome Annotation Using the RAST Pipeline","volume":"1681","author":"K McNair","year":"2018","journal-title":"Methods in molecular biology (Clifton, NJ)"},{"key":"pcbi.1008214.ref074","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1128\/MRA.00586-19","article-title":"Complete Genome Sequence of Staphylococcus aureus Siphophage Lorac","volume":"8","author":"A Marc","year":"2019","journal-title":"Microbiol Resour Announc"},{"key":"pcbi.1008214.ref075","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1128\/MRA.00054-19","article-title":"Draft Genome Sequences of Staphylococcus Podophages JBug18, Pike, Pontiff, and Pabna","volume":"8","author":"EK Culbertson","year":"2019","journal-title":"Microbiol Resour Announc"},{"key":"pcbi.1008214.ref076","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1128\/MRA.00598-19","article-title":"Complete Genome Sequences of Staphylococcus epidermidis Myophages Quidividi, Terranova, and Twillingate","volume":"8","author":"ME Freeman","year":"2019","journal-title":"Microbiol Resour Announc"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1008214","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,11,12]],"date-time":"2020-11-12T00:00:00Z","timestamp":1605139200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008214","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,12]],"date-time":"2020-11-12T19:07:41Z","timestamp":1605208061000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008214"}},"subtitle":[],"editor":[{"given":"Mihaela","family":"Pertea","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,11,2]]},"references-count":76,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2020,11,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1008214","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1008214","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,11,2]]}}}