PaVE


28053164	The Papillomavirus Episteme: a major update to the papillomavirus sequence database. [PMID: 28053164] Van Doorslaer K, Li Z, Xirasagar S, Maes P, Kaminsky D, Liou D, Sun Q, Kaur R, Huyen Y, McBride AA. 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/. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. Nucleic Acids Res. 2017:45(D1) \| 232 Citations (from Europe PMC, 2025-03-22)
23093593	The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis. [PMID: 23093593] Van Doorslaer K, Tan Q, Xirasagar S, Bandaru S, Gopalan V, Mohamoud Y, Huyen Y, McBride AA. Abstract The goal of the Papillomavirus Episteme (PaVE) is to provide an integrated resource for the analysis of papillomavirus (PV) genome sequences and related information. The PaVE is a freely accessible, web-based tool (http://pave.niaid.nih.gov) created around a relational database, which enables storage, analysis and exchange of sequence information. From a design perspective, the PaVE adopts an Open Source software approach and stresses the integration and reuse of existing tools. Reference PV genome sequences have been extracted from publicly available databases and reannotated using a custom-created tool. To date, the PaVE contains 241 annotated PV genomes, 2245 genes and regions, 2004 protein sequences and 47 protein structures, which users can explore, analyze or download. The PaVE provides scientists with the data and tools needed to accelerate scientific progress for the study and treatment of diseases caused by PVs. Nucleic Acids Res. 2013:41(Database issue) \| 146 Citations (from Europe PMC, 2025-03-22)

The Papillomavirus Episteme: a major update to the papillomavirus sequence database. [PMID: 28053164]

Van Doorslaer K, Li Z, Xirasagar S, Maes P, Kaminsky D, Liou D, Sun Q, Kaur R, Huyen Y, McBride AA.

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/. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Nucleic Acids Res. 2017:45(D1) | 232 Citations (from Europe PMC, 2025-03-22)

The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis. [PMID: 23093593]

Van Doorslaer K, Tan Q, Xirasagar S, Bandaru S, Gopalan V, Mohamoud Y, Huyen Y, McBride AA.

Abstract

The goal of the Papillomavirus Episteme (PaVE) is to provide an integrated resource for the analysis of papillomavirus (PV) genome sequences and related information. The PaVE is a freely accessible, web-based tool (http://pave.niaid.nih.gov) created around a relational database, which enables storage, analysis and exchange of sequence information. From a design perspective, the PaVE adopts an Open Source software approach and stresses the integration and reuse of existing tools. Reference PV genome sequences have been extracted from publicly available databases and reannotated using a custom-created tool. To date, the PaVE contains 241 annotated PV genomes, 2245 genes and regions, 2004 protein sequences and 47 protein structures, which users can explore, analyze or download. The PaVE provides scientists with the data and tools needed to accelerate scientific progress for the study and treatment of diseases caused by PVs.

Nucleic Acids Res. 2013:41(Database issue) | 146 Citations (from Europe PMC, 2025-03-22)

URL:	https://pave.niaid.nih.gov/
Full name:	PapillomaVirus Episteme
Description:	The PapillomaVirus Episteme (PaVE) has been established to provide highly organized and curated papillomavirus genomics information and tools to the scientific community. The PaVE consists of a database and web applications that support the storage, annotation, analysis, and exchange of information. To the extent possible, the PaVE adopts an open source software approach and emphasizes integration and reuse of existing tools. The PaVE currently contains 481 annotated papillomavirus genomes (including 105 Non-reference genomes), 4884 genes and regions, 4403 protein sequences, and 67 protein structures, which users can explore, analyze or download. The seamless integration of the data and the analytical tools is designed to assist in accelerating scientific progress and in ultimately our understanding, detection, diagnosis, and treatment of diseases caused by papillomaviruses.
Year founded:	2013
Last update:	2018-05-07
Version:	v1.1
Accessibility:	Accessible
Country/Region:	United States

Data type:	DNA Protein
Data object:	Virus
Database category:	Health and medicine Structure
Major species:	Homo sapiens
Keywords:	papillomavirus genomics Virus Taxonomy viruses virus sequences Viral Protein structures viral proteins

University/Institution:	National Institute of Allergy and Infectious Diseases
Address:	Building 33, National Institutes of Health, 33 North Drive Bethesda, MD 20892
City:	Bethesda
Province/State:	Maryland
Country/Region:	United States
Contact name (PI/Team):	Alison A. McBride
Contact email (PI/Helpdesk):	amcbride@nih.gov

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Database Commons a catalog of worldwide biological databases