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Protocols

pVOGs specifications

Information


Unique identifier OMICS_13386
Name pVOGs
Alternative name prokaryotic Virus Orthologous Groups
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Documentation


Maintainer


  • person_outline David Kristensen

Publications for prokaryotic Virus Orthologous Groups

pVOGs citations

 (5)
library_books

Characterizing Phage Genomes for Therapeutic Applications

2018
Viruses
PMCID: 5923482
PMID: 29642590
DOI: 10.3390/v10040188

[…] redicted ORF was queried by BLASTx against NCBI’s non-redundant (nr) protein sequences. Peptide sequences for each predicted ORF also underwent homology searches using BLASTp against nr, PhAnTOME [], pVOGs [] and the PHASTER Prophage/Virus databases []. The following threshold values were applied in general. Putative ORFs with 50–70% sequence identity [] to a given gene were assigned “putative.” W […]

library_books

Extension of the viral ecology in humans using viral profile hidden Markov models

2018
PLoS One
PMCID: 5774701
PMID: 29351302
DOI: 10.1371/journal.pone.0190938

[…] other tools and protocols available for detecting viral genomes in microbial genomic data. The tool Virsorter[] uses a reference set consisting of viral proteins from the RefSeq database (similar to pVOGS[]) but this tool and its database are mainly designed to detect viruses that infect microbes (archaea and bacteria).In a published protocol for virus sequence discovery for metagenomic data, Pae […]

library_books

Comparative Analysis of 37 Acinetobacter Bacteriophages

2017
Viruses
PMCID: 5795418
PMID: 29295549
DOI: 10.3390/v10010005

[…] and motifs identified using pfam_scan.pl against the Pfam31 database and InterProScan 5.25-64 [,]. Translated ORF sequences were also searched against hidden Markov model profiles downloaded from the prokaryotic Virus Orthologous Groups database [] using hmmscan [] with an e-value cut-off of 1 × 10−3. Matches to pVOG profiles were considered significant at an e-value of ≤ 1 × 10−15 and ≥35% covera […]

call_split

Comparative Genomics of Bacteriophage of the Genus Seuratvirus

2017
Genome Biol Evol
PMCID: 5758909
PMID: 29272407
DOI: 10.1093/gbe/evx275
call_split See protocol

[…] 3.6.0 using assembler only options (). The resulting genomes were annotated with Prokka 1.12 using a custom database of proteins extracted from all current viral genomes [April 2017] as well as using pVOGS (; ). Single gene phylogenetic analysis was carried out using TranslatorX to build nucleotide alignments using MAFFT, based on the aligned amino acid sequence (). Phylogenetic trees were constru […]

library_books

How to Name and Classify Your Phage: An Informal Guide

2017
Viruses
PMCID: 5408676
PMID: 28368359
DOI: 10.3390/v9040070

[…] es (uses BLASTn) [], PASC [], Gepard dotplot [].Comparison of protein groups, predicted proteomes, identification of signature genes: CoreGenes 3.5 [,], Roary (core and accessory genome analysis) [], prokaryotic Virus Orthologous Groups resource (pVOGs) [].Multiple alignment and/or phylogenetic analyses: Clustal Omega [], MUSCLE [], phylogeny.fr [], MEGA6 [], FastTree [].Visualization: progressive […]


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pVOGs institution(s)
Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA, USA; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
pVOGs funding source(s)
This work was supported by the Department of Biomedical Engineering at the University of Iowa and the Intramural Research Program of the National Library of Medicine at the National Institutes of Health.

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