PuMA: A Papillomavirus Genome Annotation Tool

Overview

Journal Virus Evol

Publisher Oxford University Press

Date 2020 Dec 31

PMID 33381306

Citations 10

Authors

Josh Pace

Ken Youens-Clark

Cordell Freeman

Bonnie Hurwitz

Koenraad Van Doorslaer

Affiliations

Soon will be listed here.

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).

Citing Articles

VITALdb: to select the best viroinformatics tools for a desired virus or application.

Koul M, Kaushik S, Singh K, Sharma D Brief Bioinform. 2025; 26(2).

PMID: 40063348 PMC: 11892104. DOI: 10.1093/bib/bbaf084.

Novel Gammapapillomavirus type in the nasal cavity of a wild red colobus (Piliocolobus tephrosceles).

Weary T, Mehta K, Goldberg T Access Microbiol. 2024; 6(8).

PMID: 39165252 PMC: 11334581. DOI: 10.1099/acmi.0.000866.v3.

Viruses in saliva from sanctuary chimpanzees (Pan troglodytes) in Republic of Congo and Uganda.

Dunay E, Rukundo J, Atencia R, Cole M, Cantwell A, Emery Thompson M PLoS One. 2023; 18(6):e0288007.

PMID: 37384730 PMC: 10310015. DOI: 10.1371/journal.pone.0288007.

Genetic Characterization of a Novel Papillomavirus Isolated from a Thoroughbred Mare.

Turco S, Gabbianelli F, Mavian C, Pietrucci D, De Paolis L, Gialletti R Viruses. 2023; 15(3).

PMID: 36992359 PMC: 10059215. DOI: 10.3390/v15030650.

Co-infection of distinct papillomavirus types in a captive North American porcupine.

Vanmechelen B, Lahoreau J, Dendauw P, Nicolier A, Maes P Virol J. 2023; 20(1):12.

PMID: 36658615 PMC: 9850686. DOI: 10.1186/s12985-023-01972-w.

References

Puustusmaa M, Abroi A . Conservation of the E8 CDS of the E8^E2 protein among mammalian papillomaviruses. J Gen Virol. 2016; 97(9):2333-2345. DOI: 10.1099/jgv.0.000526. View

Van Doorslaer K, Li Z, Xirasagar S, Maes P, Kaminsky D, Liou D . The Papillomavirus Episteme: a major update to the papillomavirus sequence database. Nucleic Acids Res. 2017; 45(D1):D499-D506. PMC: 5210616. DOI: 10.1093/nar/gkw879. View

Buck C, Day P, Trus B . The papillomavirus major capsid protein L1. Virology. 2013; 445(1-2):169-74. PMC: 3783536. DOI: 10.1016/j.virol.2013.05.038. View

Bergvall M, Melendy T, Archambault J . The E1 proteins. Virology. 2013; 445(1-2):35-56. PMC: 3811109. DOI: 10.1016/j.virol.2013.07.020. View

Vande Pol S, Klingelhutz A . Papillomavirus E6 oncoproteins. Virology. 2013; 445(1-2):115-37. PMC: 3783570. DOI: 10.1016/j.virol.2013.04.026. View

Wang J, Roden R . L2, the minor capsid protein of papillomavirus. Virology. 2013; 445(1-2):175-86. PMC: 3770800. DOI: 10.1016/j.virol.2013.04.017. View

Youens-Clark K, Bomhoff M, Ponsero A, Wood-Charlson E, Lynch J, Choi I . Erratum to: iMicrobe: Tools and data-driven discovery platform for the microbiome sciences. Gigascience. 2019; 8(8). PMC: 6675616. DOI: 10.1093/gigascience/giz097. View

Rose R, Constantinides B, Tapinos A, Robertson D, Prosperi M . Challenges in the analysis of viral metagenomes. Virus Evol. 2018; 2(2):vew022. PMC: 5822887. DOI: 10.1093/ve/vew022. View

Van Doorslaer K . Evolution of the papillomaviridae. Virology. 2013; 445(1-2):11-20. DOI: 10.1016/j.virol.2013.05.012. View

10.

Bernard H . Regulatory elements in the viral genome. Virology. 2013; 445(1-2):197-204. DOI: 10.1016/j.virol.2013.04.035. View

11.

Altschul S, Wootton J, Gertz E, Agarwala R, Morgulis A, Schaffer A . Protein database searches using compositionally adjusted substitution matrices. FEBS J. 2005; 272(20):5101-9. PMC: 1343503. DOI: 10.1111/j.1742-4658.2005.04945.x. View

12.

Lopez-Bueno A, Mavian C, Labella A, Castro D, Borrego J, Alcami A . Concurrence of Iridovirus, Polyomavirus, and a Unique Member of a New Group of Fish Papillomaviruses in Lymphocystis Disease-Affected Gilthead Sea Bream. J Virol. 2016; 90(19):8768-79. PMC: 5021401. DOI: 10.1128/JVI.01369-16. View

13.

Woolhouse M, Scott F, Hudson Z, Howey R, Chase-Topping M . Human viruses: discovery and emergence. Philos Trans R Soc Lond B Biol Sci. 2012; 367(1604):2864-71. PMC: 3427559. DOI: 10.1098/rstb.2011.0354. View

14.

Cock P, Antao T, Chang J, Chapman B, Cox C, Dalke A . Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009; 25(11):1422-3. PMC: 2682512. DOI: 10.1093/bioinformatics/btp163. View

15.

Grant C, Bailey T, Noble W . FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011; 27(7):1017-8. PMC: 3065696. DOI: 10.1093/bioinformatics/btr064. View

16.

Enquist L . Virology in the 21st century. J Virol. 2009; 83(11):5296-308. PMC: 2681991. DOI: 10.1128/JVI.00151-09. View

17.

Graham S, Faizo A . Control of human papillomavirus gene expression by alternative splicing. Virus Res. 2016; 231:83-95. PMC: 5335905. DOI: 10.1016/j.virusres.2016.11.016. View

18.

Roman A, Munger K . The papillomavirus E7 proteins. Virology. 2013; 445(1-2):138-68. PMC: 3783579. DOI: 10.1016/j.virol.2013.04.013. View

19.

McBride A . The papillomavirus E2 proteins. Virology. 2013; 445(1-2):57-79. PMC: 3783563. DOI: 10.1016/j.virol.2013.06.006. View

20.

Bailey T, Elkan C . Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994; 2:28-36. View