PuMA

PuMA annotates papillomavirus genomes by automatically identifying and annotating viral features from high-throughput sequencing data for viral metagenomics analyses.

Key Features:

• Automated Genome Annotation: Provides automated annotation of papillomavirus genomes, producing feature calls from sequence data.
• High Accuracy: Achieves 98% agreement when benchmarked against 481 reference genomes in the papillomavirus episteme (PaVE).
• Extensive Annotation Capability: Annotated 1,424 viral features across 168 newly isolated papillomaviruses in reported applications.
• General Applicability: A version of PuMA has been applied to annotate polyomaviruses in addition to papillomaviruses.

Scientific Applications:

• Genome annotation and reconstruction: Enables reconstruction and annotation of novel papillomavirus genomes from sequencing data.
• Taxonomic classification: Supports classification of newly identified papillomaviruses within comparative reference frameworks.
• Viral diversity and evolution studies: Facilitates metagenomic surveys and evolutionary analyses to expand understanding of papillomavirus diversity, genomic organization, and functional characteristics.

Methodology:

PuMA employs an automated computational approach to annotate papillomavirus genomes using high-throughput sequencing data.