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

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

doi:10.1093/nar/gkw1030

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

Journal Article · Sun Oct 30 00:00:00 EDT 2016 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkw1030· OSTI ID:1379663

Paez-Espino, David ^[1]; Chen, I. -Min A. ^[2]; Palaniappan, Krishna ^[2]; Ratner, Anna ^[2]; Chu, Ken ^[2]; Szeto, Ernest ^[2]; Pillay, Manoj ^[2]; Huang, Jinghua ^[2]; Markowitz, Victor M. ^[2]; Nielsen, Torben ^[1]; Huntemann, Marcel ^[1]; K. Reddy, T. B. ^[1]; Pavlopoulos, Georgios A. ^[1]; Sullivan, Matthew B. ^[3]; Campbell, Barbara J. ^[4]; Chen, Feng ^[5]; McMahon, Katherine ^[6]; Hallam, Steve J. ^[7]; Denef, Vincent ^[8]; Cavicchioli, Ricardo ^[9] more »

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center
The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology and Civil Environmental and Geodetic Engineering
Clemson Univ., SC (United States). Dept. of Biological Sciences
Univ. of Maryland Center for Environmental Sciences, Baltimore, MD (United States). Inst. of Marine and Environmental Technology
Univ. of Wisconsin, Madison, WI (United States). Dept. of Bacteriology, Dept. of Civil and Environmental Engineering
Univ. of British Columbia, Vancouver, BC (Canada). Dept. of Microbiology and Immunology, Genome Science, Technology and Program in Bioinformatics, Peter Wall Inst. for Advanced Studies, ECOSCOPE Training Program
Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Ecology and Evolutionary Biology
Univ. of New South Wales, Sydney, NSW (Australia). School of biotechnology and Biomolecular Sciences
Univ. of Calgary, AB (Canada). Dept. of Biological Sciences
Univ. of Hamburg (Germany). Dept. of Microbiology and Biotechnology
Univ. of Auckland (New Zealand). School of Biological Sciences
Agricultural Research, Education and Extension Organization, Karaj (Iran). Dept. of Systems Biology
Shell International Exploration and Production Inc., Houston, TX (United States)
Univ. of Sao Paulo (Brazil). Dept. of Biochemistry,
Norwegian Univ. of Life Sciences, As (Norway+. Dept. of Chemistry, Biotechnology, and Food Science
Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Civil and Environmental Engineering

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1379663

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 45; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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

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