PuMA: A papillomavirus genome annotation tool

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Author
Pace, J.
Youens-Clark, K.
Freeman, C.
Hurwitz, B.
Van Doorslaer, K.
Affiliation
School of Animal and Comparative Biomedical Sciences, University of Arizona
Department of Biomedical Engineering, University of Arizona
Department of Electrical and Computer Engineering, University of Arizona
The BIO5 Institute, University of Arizona
Department of Immunobiology, Cancer Biology GIDP, Genetics GIDP, UA Cancer Center, University of Arizona
Issue Date
2020
Keywords
Annotation
High-throughput sequencing
Metagenomics
Papillomavirus
Polyomavirus
Virome

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Publisher
Oxford University Press
Citation
Pace, J., Youens-Clark, K., Freeman, C., Hurwitz, B., & Van Doorslaer, K. (2020). PuMA: a papillomavirus genome annotation tool. Virus Evolution, 6(2), veaa068.
Journal
Virus Evolution
Rights
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/).
Collection Information
This 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.
Abstract
High-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.
Note
Open access journal
ISSN
2057-1577
DOI
10.1093/ve/veaa068
Version
Final published version
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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/).