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iVirus specifications

Information


Unique identifier OMICS_13484
Name iVirus
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Bonnie Hurwitz

Publication for iVirus

iVirus citations

 (5)
library_books

Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches

2017
Viruses
PMCID: 5490804
PMID: 28538703
DOI: 10.3390/v9060127

[…] ction of viral sequences in metagenomic data; VirusSeeker, released in early 2017 (mainly focused on eukaryotic viruses, though it does incorporate bacteriophage analysis in the pipeline []); and the iVirus community resource, which provides access to a range of viral metagenomic tools and datasets []. Thus, as methods improve, the discrepancies and biases introduced by these programs will hopeful […]

library_books

Intriguing Interaction of Bacteriophage Host Association: An Understanding in the Era of Omics

2017
Front Microbiol
PMCID: 5383658
PMID: 28439260
DOI: 10.3389/fmicb.2017.00559

[…] or annotation of viral genomes, a database such as NCBI non-redundant nucleotides can be used. ORFs can be determined and annotated using CyVerse (Goff et al., ) in the PCPipe application through the iVirus project (Hurwitz et al., ).Bioinformatic tools mine enormous volume of sequence data to determine common patterns that govern microbes in an ecosystem. Viral diversity can be estimated using PH […]

call_split

Alignment free \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{ 69pt} \begin{document} }{}$d_2^*$\end{document} oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically derived viral sequences

2016
Nucleic Acids Res
PMCID: 5224470
PMID: 27899557
DOI: 10.1093/nar/gkw1002
call_split See protocol

[…] s and their associated taxonomies used previously in Roux et al. () were made available by the authors and downloaded from iPlant at http://mirrors.iplantcollaborative.org/download/iplant/home/shared/ivirus/VirSorter_curated_dataset/. SUP05 virus genomes assembled from metagenomes from hydrothermal vent plume samples () and the crAssphage genome assembled from human gut metagenomes () were downloa […]

library_books

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

2016
Front Microbiol
PMCID: 4899465
PMID: 27375564
DOI: 10.3389/fmicb.2016.00822

[…] es and CAMERA was discontinued in 2014. Since then, CAMERA's sequence data has been transferred to the iMicrobe portal (http://imicrobe.us/, supported by iPlant) and although iMicrobe, and its cousin iVirus (still under development), are likely to be valuable resources, they are not currently funded to accommodate the petabytes of data being produced by the community.Metavir, launched in 2011 as a […]

library_books

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

2015
eLife
PMCID: 4533152
PMID: 26200428
DOI: 10.7554/eLife.08490.023

[…] filiation of predicted genes, etc) and extract a specific subset of interest (these tools are under the tab ‘Contig maps’). Nucleotide sequences from the VirSorter curated data set are also hosted at iVirus, alongside the viral clusters annotation and network (as cytoscape-ready text files), the virus–host matrix, and the complete list of viral sequence predictions in the 14,977 archaeal and bacte […]

Citations

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iVirus institution(s)
Department of Microbiology, The Ohio State University, Columbus, OH, USA; Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ, USA; Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
iVirus funding source(s)
This work was funded by Gordon and Betty Moore Foundation Grants GBMF4491, GBMF4733, GBMF3305 and GBMF3790, by the US Department of Energy Office of Biological and Environmental Research under the Genomic Science program (Award DE- SC0010580) and by a TRIF award to the University of Arizona Ecosystem Genomics Initiative.

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