ViPR: an open bioinformatics database and analysis resource for virology research

By B. Pickett, E. Sadat, Yun Zhang, J. Noronha, R. B. Squires, Victoria Hunt, Mengya Liu, Sanjeev Kumar, S. Zaremba, Z. Gu and 5 more. Nucleic Acids Res., 2011

658 citations recorded by the source corpus.

The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR contains information for human pathogenic viruses belonging to the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae and Togaviridae families, with plans to support additional virus families in the future. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. Analytical and visualization tools for metadata-driven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison and sequence variation determination are also provided. Data filtering and analysis workflows can be combined and the results saved in personal ‘Workbenches’ for future use. ViPR tools and data are available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.

Subfields: Infectious Diseases, Plant Science, Public Health, Environmental and Occupational Health

View Paper: https://www.semanticscholar.org/paper/83e21271aa794fd03ec49c059ec6fb831307a3b5

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In Infectious Diseases

Alessandro Sette

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Citations in the corpus

Molecular Evolution of Human Coronavirus Genomes (2016, neutral): “, The Virus Pathogen Database and Analysis Resource, ViPR [65]).”
Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies (2020, methodology): “Similar to T cell epitopes, we used in our study the SARS-CoV-derived B cell epitopes that have been experimentallydetermined from B cell-positive assays (Pickett et al., 2012).”
Rfam 14: expanded coverage of metagenomic, viral and microRNA families (2020, methodology): “The method is based on clustering the set of available complete genomes in ViPR (29) and RefSeq (8) and calculating highquality genome alignments of representative viruses.”
Monkeypox Virus in Nigeria: Infection Biology, Epidemiology, and Evolution (2020, neutral): “Genomes of five Nigerian isolates (MPXV-3019, MPXV3020, MPXV-3025, MPXV-3029, MPXV-3030) were from 2017 outbreak in Rivers State [60] and the two other genomes from Nigeria isolates (MPXV-SE-Nigeria, MPXV-W-Nigeria) were from earlier outbreaks in 1971 (Abia State) and 1978 (Oyo State), respectively ”
Virus Variation Resource – improved response to emergent viral outbreaks (2016, background): “In many ways, the NCBI Influenza Virus Resource paved a path for a variety of other resources that share the common goal of making viral sequence data more accessible (9) (10) (11) (12) .”
UniProt: a worldwide hub of protein knowledge (2018, background): “We compiled and curated complete viral genome (proteome) data from INSDC (which feeds into UniProt) as well as a range of other specialized viral genome resources including ViPr (9), IRD (10), the HIV database (https://www.hiv.lanl. gov/), Papillomavirus Episteme (11) and the HCV database (https://h”
NCBI Viral Genomes Resource (2014, background): “These collaborations often include members of the UniProt Viral Protein Annotation Program (45) (9), and/or curators from sequencing centers and other databases (46) in addition to members of the relevant viral communities and effectively ensure both well annotated references and consistently annota”
A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2 (2020, positive): “The Virus Pathogen Resource (ViPR) is a complementary repository of information about human pathogenic viruses that integrates genome, gene, and protein sequence information with data about immune epitopes, protein structures, and host responses to virus infections (Pickett et al., 2012).”