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PuMA: A papillomavirus genome annotation tool

dc.contributor.authorPace, J.
dc.contributor.authorYouens-Clark, K.
dc.contributor.authorFreeman, C.
dc.contributor.authorHurwitz, B.
dc.contributor.authorVan Doorslaer, K.
dc.date.accessioned2021-06-05T02:35:03Z
dc.date.available2021-06-05T02:35:03Z
dc.date.issued2020
dc.identifier.citationPace, J., Youens-Clark, K., Freeman, C., Hurwitz, B., & Van Doorslaer, K. (2020). PuMA: a papillomavirus genome annotation tool. Virus Evolution, 6(2), veaa068.
dc.identifier.issn2057-1577
dc.identifier.doi10.1093/ve/veaa068
dc.identifier.urihttp://hdl.handle.net/10150/659758
dc.description.abstractHigh-throughput sequencing technologies provide unprecedented power to identify novel viruses from a wide variety of (environmental) samples. The field of 'viral metagenomics' has dramatically expanded our understanding of viral diversity. Viral metagenomic approaches imply that many novel viruses will not be described by researchers who are experts on (the genomic organization of) that virus family. We have developed the papillomavirus annotation tool (PuMA) to provide researchers with a convenient and reproducible method to annotate and report novel papillomaviruses. PuMA currently correctly annotates 99% of the papillomavirus genes when benchmarked against the 655 reference genomes in the papillomavirus episteme. Compared to another viral annotation pipeline, PuMA annotates more viral features while being more accurate. To demonstrate its general applicability, we also developed a preliminary version of PuMA that can annotate polyomaviruses. PuMA is available on GitHub (https://github.com/KVD-lab/puma) and through the iMicrobe online environment (https://www.imicrobe.us/#/apps/puma). © The Author(s) 2020.
dc.language.isoen
dc.publisherOxford University Press
dc.rightsCopyright © The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectAnnotation
dc.subjectHigh-throughput sequencing
dc.subjectMetagenomics
dc.subjectPapillomavirus
dc.subjectPolyomavirus
dc.subjectVirome
dc.titlePuMA: A papillomavirus genome annotation tool
dc.typeArticle
dc.typetext
dc.contributor.departmentSchool of Animal and Comparative Biomedical Sciences, University of Arizona
dc.contributor.departmentDepartment of Biomedical Engineering, University of Arizona
dc.contributor.departmentDepartment of Electrical and Computer Engineering, University of Arizona
dc.contributor.departmentThe BIO5 Institute, University of Arizona
dc.contributor.departmentDepartment of Immunobiology, Cancer Biology GIDP, Genetics GIDP, UA Cancer Center, University of Arizona
dc.identifier.journalVirus Evolution
dc.description.noteOpen access journal
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.
dc.eprint.versionFinal published version
dc.source.journaltitleVirus Evolution
refterms.dateFOA2021-06-05T02:35:03Z


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Copyright © The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).
Except where otherwise noted, this item's license is described as Copyright © The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).