RT Journal Article
SR Electronic
T1 PuMA: a papillomavirus genome annotation tool
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 736991
DO 10.1101/736991
A1 J. Pace
A1 K. Youens-Clark
A1 C. Freeman
A1 B. Hurwitz
A1 K. Van Doorslaer
YR 2019
UL http://biorxiv.org/content/early/2019/08/16/736991.abstract
AB 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. There is a need to develop analytical approaches to reconstruct, annotate, and classify viral genomes. We have developed the papillomavirus annotation tool (PuMA) to provide researchers with a convenient and reproducible method to annotate novel papillomaviruses. PuMA provides an accessible method for automated papillomavirus genome annotation. PuMA currently has a 98% accuracy when benchmarked against the 481 reference genomes in the papillomavirus episteme (PaVE). Finally, PuMA was used to annotate 168 newly isolated papillomaviruses, and successfully annotated 1424 viral features. To demonstrate its general applicability, we developed a 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)