IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Paez-Espino, D; Chen, I-MA; Palaniappan, K; Ratner, A; Chu, K; Szeto, E; Pillay, M; Huang, J; Markowitz, VM; Nielsen, T; Huntemann, M; K Reddy, TB; Pavlopoulos, GA; Sullivan, MB; Campbell, BJ; Chen, F; McMahon, K; Hallam, SJ; Denef, V; Cavicchioli, R; Caffrey, SM; Streit, WR; Webster, J; Handley, KM; Salekdeh, GH; Tsesmetzis, N; Setubal, JC; Pope, PB; Liu, W-T; Rivers, AR; Ivanova, NN; Kyrpides, NC

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Paez-Espino, D Chen, I-MA Palaniappan, K Ratner, A Chu, K Szeto, E Pillay, M Huang, J Markowitz, VM Nielsen, T Huntemann, M K Reddy, TB Pavlopoulos, GA Sullivan, MB Campbell, BJ Chen, F McMahon, K Hallam, SJ Denef, V Cavicchioli, R Caffrey, SM Streit, WR Webster, J Handley, KM Salekdeh, GH Tsesmetzis, N Setubal, JC Pope, PB Liu, W-T Rivers, AR Ivanova, NN Kyrpides, NC

Permalink

Publisher:: Oxford University Press
Publication Type:: Journal Article
Citation:: Nucleic Acids Research, 2017, 45, (D1), pp. D457-D465
Issue Date:: 2017-01-04

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Adobe PDF

Download full textAdobe PDF (5.82 MB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Paez-Espino, D
dc.contributor.author	Chen, I-MA
dc.contributor.author	Palaniappan, K
dc.contributor.author	Ratner, A
dc.contributor.author	Chu, K
dc.contributor.author	Szeto, E
dc.contributor.author	Pillay, M
dc.contributor.author	Huang, J
dc.contributor.author	Markowitz, VM
dc.contributor.author	Nielsen, T
dc.contributor.author	Huntemann, M
dc.contributor.author	K Reddy, TB
dc.contributor.author	Pavlopoulos, GA
dc.contributor.author	Sullivan, MB
dc.contributor.author	Campbell, BJ
dc.contributor.author	Chen, F
dc.contributor.author	McMahon, K
dc.contributor.author	Hallam, SJ
dc.contributor.author	Denef, V
dc.contributor.author	Cavicchioli, R
dc.contributor.author	Caffrey, SM
dc.contributor.author	Streit, WR
dc.contributor.author	Webster, J
dc.contributor.author	Handley, KM
dc.contributor.author	Salekdeh, GH
dc.contributor.author	Tsesmetzis, N
dc.contributor.author	Setubal, JC
dc.contributor.author	Pope, PB
dc.contributor.author	Liu, W-T
dc.contributor.author	Rivers, AR
dc.contributor.author	Ivanova, NN
dc.contributor.author	Kyrpides, NC
dc.date.accessioned	2022-09-13T04:52:49Z
dc.date.available	2016-10-27
dc.date.available	2022-09-13T04:52:49Z
dc.date.issued	2017-01-04
dc.identifier.citation	Nucleic Acids Research, 2017, 45, (D1), pp. D457-D465
dc.identifier.issn	0305-1048
dc.identifier.issn	1362-4962
dc.identifier.uri	http://hdl.handle.net/10453/161782
dc.description.abstract	Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.
dc.format	Print-Electronic
dc.language	eng
dc.publisher	Oxford University Press
dc.relation.ispartof	Nucleic Acids Research
dc.relation.isbasedon	10.1093/nar/gkw1030
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	05 Environmental Sciences, 06 Biological Sciences, 08 Information and Computing Sciences
dc.subject.classification	Developmental Biology
dc.subject.mesh	Databases, Genetic
dc.subject.mesh	DNA Viruses
dc.subject.mesh	Environmental Microbiology
dc.subject.mesh	Genome, Viral
dc.subject.mesh	Genomics
dc.subject.mesh	Host-Pathogen Interactions
dc.subject.mesh	Metagenome
dc.subject.mesh	Metagenomics
dc.subject.mesh	Retroviridae
dc.subject.mesh	Sequence Analysis, DNA
dc.subject.mesh	Software
dc.subject.mesh	DNA Viruses
dc.subject.mesh	Databases, Genetic
dc.subject.mesh	Environmental Microbiology
dc.subject.mesh	Genome, Viral
dc.subject.mesh	Genomics
dc.subject.mesh	Host-Pathogen Interactions
dc.subject.mesh	Metagenome
dc.subject.mesh	Metagenomics
dc.subject.mesh	Retroviridae
dc.subject.mesh	Sequence Analysis, DNA
dc.subject.mesh	Software
dc.subject.mesh	DNA Viruses
dc.subject.mesh	Retroviridae
dc.subject.mesh	Sequence Analysis, DNA
dc.subject.mesh	Genomics
dc.subject.mesh	Environmental Microbiology
dc.subject.mesh	Genome, Viral
dc.subject.mesh	Software
dc.subject.mesh	Databases, Genetic
dc.subject.mesh	Host-Pathogen Interactions
dc.subject.mesh	Metagenome
dc.subject.mesh	Metagenomics
dc.title	IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.
dc.type	Journal Article
utslib.citation.volume	45
utslib.location.activity	England
utslib.for	05 Environmental Sciences
utslib.for	06 Biological Sciences
utslib.for	08 Information and Computing Sciences
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
utslib.copyright.status	open_access	*
pubs.consider-herdc	false
dc.date.updated	2022-09-13T04:52:43Z
pubs.issue	D1
pubs.publication-status	Published
pubs.volume	45
utslib.citation.issue	D1

Abstract:

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/161782