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Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.

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

Author information

1
Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
2
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
3
Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA.
4
Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA.
5
Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA.
6
Department of Civil and Environmental Engineering, Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.
7
Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
8
Genome Science, Technology, and Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
9
Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, BC V6T 1Z2, Canada.
10
ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 0A1, Canada.
11
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA.
12
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
13
Department of Biological Sciences, University of Calgary, Calgary, AB T2N 4V8, Canada.
14
Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg 22609, Germany.
15
School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
16
Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj 31535-1897, Iran.
17
Shell International Exploration and Production Inc., Houston, TX 77082, USA.
18
Department of Biochemistry, Institute of Chemistry, Universidade de Sao Paulo, SP 05508-000, Brazil.
19
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1432, Norway.
20
Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
21
Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA nckyrpides@lbl.gov.

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.

PMID:
27799466
PMCID:
PMC5210529
DOI:
10.1093/nar/gkw1030
[Indexed for MEDLINE]
Free PMC Article

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