The Papillomavirus Episteme: a major update to the papillomavirus sequence database

Abstract

The Papillomavirus Episteme (PaVE) is a database of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. This update describes the addition of major new features. The papillomavirus genomes within PaVE have been further annotated, and now includes the major spliced mRNA transcripts. Viral genes and transcripts can be visualized on both linear and circular genome browsers. Evolutionary relationships among PaVE reference protein sequences can be analysed using multiple sequence alignments and phylogenetic trees. To assist in viral discovery, PaVE offers a typing tool; a simplified algorithm to determine whether a newly sequenced virus is novel. PaVE also now contains an image library containing gross clinical and histopathological images of papillomavirus infected lesions. Database URL: https://pave.niaid.nih.gov/.

Figure 1.

Information Architecture of the PaVE Web Resource. Architecture of the redesigned PaVE web interface, showing the three main ways to access the data and tools using the concepts of ‘Search, ‘Analyse’ and ‘Explore’.

Figure 2.

Circular genome browser. The PaVE locus view allows users to toggle between a linear and circular (shown here) representation of the viral genome. Viral features annotated to HPV204 are shown and can be selected. The ‘selected feature details’ window displays additional information about the ORF. The ‘coding region sequences’ window shows the nucleotide sequence for the selected ORF. Sequences can be further analysed using BLAST or the PaVE structure viewer (1). Finally, the relative position of the selected feature is displayed.

Figure 3.

Integrated calculation of multiple sequence alignments and phylogenetic trees. An example of a typical analysis is shown. (A) Filters and pull-down menus on the PaVE search page are used to select the protein sequences of interest. The applied filters are indicated in the orange box. Sequences can be selected and used for the construction of a multiple sequence alignment or phylogenetic tree. (B) The first 80 amino-acids of a Cobalt based multiple sequence alignment of the E2 proteins of nine highly divergent papillomaviruses is shown as displayed within Jalview. Residues are coloured according to Clustal X. (C) The Neighbour-joining phylogenetic tree is displayed using JsPhyloSVG (39). If available, viral genera are included.

Figure 4.

PaVE image database. PaVE has collected images related to papillomavirus infections. These can be browsed using the PaVE Image Viewer. (A) A screenshot of thumbnails in a portion of the image gallery. (B) Oral papillomatous lesions in a coyote. Courtesy of Kevin Keel, UC Davis School of Veterinary Medicine. (C) H&E stain of a canine inverted papilloma. Courtesy of Patricia Pesavento, UC Davis School of Veterinary Medicine.

Figure 5.

L1 based taxonomic classification. The PaVE taxonomy tool is designed to aid researchers in preliminary classification of novel papillomaviruses. (A) The tool accepts the L1 nucleotide sequence in FastA format. The sequence can be uploaded, or pasted into the search box. (B) Results are summarized, and more detailed information is provided, in multiple formats. (C) The phylogenetic position of the submitted L1 sequence is displayed. For representation purposes, the tree was cropped from the full tree. Dotted lines indicate that the tree continues along the indicated branch.