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

  • Author(s): 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
  • et al.
Abstract

© The Author(s) 2016. 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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