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

Koenraad Van Doorslaer; Zhiwen Li; Sandhya Xirasagar; Piet Maes; David Kaminsky; David Liou; Qiang Sun; Ramandeep Kaur; Yentram Huyen; Alison A. McBride

doi:10.1093/nar/gkw879

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

Koenraad Van Doorslaer, Zhiwen Li, Sandhya Xirasagar, Piet Maes, David Kaminsky, David Liou, Qiang Sun, Ramandeep Kaur, Yentram Huyen, Alison A. McBride

Research output: Contribution to journal › Article › peer-review

300 Scopus citations

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/.

Original language	English (US)
Pages (from-to)	D499-D506
Journal	Nucleic acids research
Volume	45
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkw879
State	Published - Jan 1 2017

ASJC Scopus subject areas

Genetics

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title = "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/.",

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AU - Maes, Piet

AU - Kaminsky, David

AU - Liou, David

AU - Sun, Qiang

AU - Kaur, Ramandeep

AU - Huyen, Yentram

AU - McBride, Alison A.

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

Abstract

ASJC Scopus subject areas

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