IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses

David Paez-Espino; I. Min A. Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; Ernest Szeto; Manoj Pillay; Jinghua Huang; Victor M. Markowitz; Torben Nielsen; Marcel Huntemann; T. B.K. Reddy; Georgios A. Pavlopoulos; Matthew B. Sullivan; Barbara J. Campbell; Feng Chen; Katherine McMahon; Steve J. Hallam; Vincent Denef; Ricardo Cavicchioli; Sean M. Caffrey; Wolfgang R. Streit; John Webster; Kim M. Handley; Ghasem H. Salekdeh; Nicolas Tsesmetzis; Joao C. Setubal; Phillip B. Pope; Wen Tso Liu; Adam R. Rivers; Natalia N. Ivanova; Nikos C. Kyrpides

doi:10.1093/nar/gkw1030

IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses

David Paez-Espino, I. Min A. Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, Ernest Szeto, Manoj Pillay, Jinghua Huang, Victor M. Markowitz, Torben Nielsen, Marcel Huntemann, T. B.K. Reddy, Georgios A. Pavlopoulos, Matthew B. Sullivan, Barbara J. Campbell, Feng Chen, Katherine McMahon, Steve J. Hallam, Vincent Denef, Ricardo CavicchioliSean M. Caffrey, Wolfgang R. Streit, John Webster, Kim M. Handley, Ghasem H. Salekdeh, Nicolas Tsesmetzis, Joao C. Setubal, Phillip B. Pope, Wen Tso Liu, Adam R. Rivers, Natalia N. Ivanova, Nikos C. Kyrpides

Ecology and Evolutionary Biology

Research output: Contribution to journal › Article › peer-review

142 Scopus citations

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 comparingwith external sequences, thus serving as an essential resource in the viral genomics community.

Original language	English (US)
Pages (from-to)	D457-D465
Journal	Nucleic acids research
Volume	45
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkw1030
State	Published - Jan 1 2017

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkw1030

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Paez-Espino, D., Chen, I. M. A., Palaniappan, K., Ratner, A., Chu, K., Szeto, E., Pillay, M., Huang, J., Markowitz, V. M., Nielsen, T., Huntemann, M., Reddy, T. B. K., Pavlopoulos, G. A., Sullivan, M. B., Campbell, B. J., Chen, F., McMahon, K., Hallam, S. J., Denef, V., ... Kyrpides, N. C. (2017). IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses. Nucleic acids research, 45(D1), D457-D465. https://doi.org/10.1093/nar/gkw1030

Paez-Espino, D, Chen, IMA, Palaniappan, K, Ratner, A, Chu, K, Szeto, E, Pillay, M, Huang, J, Markowitz, VM, Nielsen, T, Huntemann, M, Reddy, TBK, 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, WT, Rivers, AR, Ivanova, NN & Kyrpides, NC 2017, 'IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses', Nucleic acids research, vol. 45, no. D1, pp. D457-D465. https://doi.org/10.1093/nar/gkw1030

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title = "IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses",

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 comparingwith external sequences, thus serving as an essential resource in the viral genomics community.",

author = "David Paez-Espino and Chen, {I. Min A.} and Krishna Palaniappan and Anna Ratner and Ken Chu and Ernest Szeto and Manoj Pillay and Jinghua Huang and Markowitz, {Victor M.} and Torben Nielsen and Marcel Huntemann and Reddy, {T. B.K.} and Pavlopoulos, {Georgios A.} and Sullivan, {Matthew B.} and Campbell, {Barbara J.} and Feng Chen and Katherine McMahon and Hallam, {Steve J.} and Vincent Denef and Ricardo Cavicchioli and Caffrey, {Sean M.} and Streit, {Wolfgang R.} and John Webster and Handley, {Kim M.} and Salekdeh, {Ghasem H.} and Nicolas Tsesmetzis and Setubal, {Joao C.} and Pope, {Phillip B.} and Liu, {Wen Tso} and Rivers, {Adam R.} and Ivanova, {Natalia N.} and Kyrpides, {Nikos C.}",

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doi = "10.1093/nar/gkw1030",

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AU - Paez-Espino, David

AU - Chen, I. Min A.

AU - Palaniappan, Krishna

AU - Ratner, Anna

AU - Chu, Ken

AU - Szeto, Ernest

AU - Pillay, Manoj

AU - Huang, Jinghua

AU - Markowitz, Victor M.

AU - Nielsen, Torben

AU - Huntemann, Marcel

AU - Reddy, T. B.K.

AU - Pavlopoulos, Georgios A.

AU - Sullivan, Matthew B.

AU - Campbell, Barbara J.

AU - Chen, Feng

AU - McMahon, Katherine

AU - Hallam, Steve J.

AU - Denef, Vincent

AU - Cavicchioli, Ricardo

AU - Caffrey, Sean M.

AU - Streit, Wolfgang R.

AU - Webster, John

AU - Handley, Kim M.

AU - Salekdeh, Ghasem H.

AU - Tsesmetzis, Nicolas

AU - Setubal, Joao C.

AU - Pope, Phillip B.

AU - Liu, Wen Tso

AU - Rivers, Adam R.

AU - Ivanova, Natalia N.

AU - Kyrpides, Nikos C.

PY - 2017/1/1

Y1 - 2017/1/1

N2 - 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 comparingwith external sequences, thus serving as an essential resource in the viral genomics community.

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IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses

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