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Protocols

ViPR specifications

Information


Unique identifier OMICS_03087
Name ViPR
Alternative name Virus Pathogen database and analysis Resource
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Virus_Pathogen_Database_and_Analysis_Resource

Maintainer


  • person_outline Richard H. Scheuermann

Publication for Virus Pathogen database and analysis Resource

ViPR citations

 (18)
library_books

The Effects of Sampling Location and Predictor Point Estimate Certainty on Posterior Support in Bayesian Phylogeographic Generalized Linear Models

2018
Sci Rep
PMCID: 5897398
PMID: 29651124
DOI: 10.1038/s41598-018-24264-8

[…] We obtained whole genome WNV sequences from the Virus Pathogen Database and Analysis Resource using the following search criteria: Family = Flaviviridae, Genus = Flavivirus, Species = West Nile Virus, Collection Year = 1999–2012, Geography = USA, H […]

call_split

Origin and dispersal of Hepatitis E virus

2018
PMCID: 5837148
PMID: 29410449
DOI: 10.1038/s41426-017-0009-6
call_split See protocol

[…] we also used a sub-region of Reg-2 (denoted Reg-2-short). Reg-2-short was selected to maximize the number of available African and South/Central American sequences. In particular, we downloaded from ViPR all HEV genome fragments longer than 300 nucleotides and deriving from sequences isolated in Africa and South/Central America. We aligned these fragments to complete HEV genomes and selected the […]

library_books

Probing the antigenicity of hepatitis C virus envelope glycoprotein complex by high throughput mutagenesis

2017
PLoS Pathog
PMCID: 5749897
PMID: 29253863
DOI: 10.1371/journal.ppat.1006735

[…] For amino-acid conservation, data were obtained from the NIAID Virus Pathogen Database and Analysis Resource (ViPR) online through the web site at http://www.viprbrc.org []. 2,345 complete genomes encompassing genotypes 1 through 7 as well as 52 unclassified geno […]

library_books

A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi genotype mixed infection

2017
BMC Genomics
PMCID: 5404283
PMID: 28438140
DOI: 10.1186/s12864-017-3714-6

[…] e constellation, and a representative subsample of G1P8 RoV with a Wa-like backbone (I1-R1-C1-M1-A1-N1-T1-E1-H1) and G2P4 RoV with a DS-1-like backbone were obtained from the Virus Pathogen Resource (ViPR) database (http://www.viprbrc.org/), and manually aligned using Geneious (v9.0). Segment-specific maximum likelihood (ML) trees were then inferred using RAxML [] under the GTRGAMMA model with 500 […]

library_books

Point of sampling detection of Zika virus within a multiplexed kit capable of detecting dengue and chikungunya

2017
BMC Infect Dis
PMCID: 5399334
PMID: 28427352
DOI: 10.1186/s12879-017-2382-0

[…] the evolutionary variation within the genomes of viral targets. Viral sequences for dengue-1 were downloaded from the Broad Institute [], while those for other targets were downloaded from the NIAID Virus Pathogen Database and Analysis Resource (ViPR) []. Multiple sequence alignments (MSAs) were created for these sequences using MUSCLE v3.8.31 []. The resulting MSAs were used as input to OligArch […]

library_books

Pathogen metadata platform: software for accessing and analyzing pathogen strain information

2016
BMC Bioinformatics
PMCID: 5025631
PMID: 27634291
DOI: 10.1186/s12859-016-1231-2

[…] ubmission of nucleotide sequence data. BioSample and BioProject databases exchange data with their European and Japanese counterparts []. The Pathosystems Resource Integration Center (PATRIC) and the Virus Pathogen Database and Analysis Resource (ViPR) also provide standardized metadata for some pathogenic bacterial and viral genomes, respectively [, ]. The Genomes Online Database (GOLD) [], devel […]

Citations

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ViPR institution(s)
Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Statistical Science, Southern Methodist University, Dallas, TX, USA; Northrop Grumman Health IT Systems, Rockville, MD, USA; Vecna Technologies, Greenbelt, MD, USA; Division of Biomedical Informatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
ViPR funding source(s)
Supported by N01-AI2008038 from the US National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services.

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