ViPTree : the Viral Proteomic Tree server    version 1.4

About

The ViPTree server generates a "proteomic tree" of viral genome sequences based on genome-wide sequence similarities computed by tBLASTx. The original proteomic tree concept (i.e., "the Phage Proteomic Tree”) was developed by Rohwer and Edwards, 2002. A proteomic tree is a dendrogram that reveals global genomic similarity relationships between tens, hundreds, and thousands of viruses. It has been shown that viral groups identified in a proteomic tree well correspond to established viral taxonomies. The proteomic tree approach is effective to investigate genomes of newly sequenced viruses as well as those identified in metagenomes.

Workflow

Browse trees of reference viral genomes

  1. Select nucleic acid types: dsDNA / ssDNA / dsRNA / ssRNA viruses / retroviruses / satellite viruses and virophages
  2. Select host categories: prokaryotic / eukaryotic / any host
  3. Browse proteomic trees and genomic alignments between reference viruses
  4. Download figures and tables

Generate a proteomic tree of your viruses

  1. Upload your viral sequences and choose reference viruses to generate a proteomic tree
  2. Browse the proteomic tree
  3. Regenerate a focused proteomic tree only with viruses selected from the entire proteomic tree for interpretation / presentation
  4. Browse dotplots / genomic alignments between your viruses and reference viruses
  5. Browse genomic similarity scores and gene annotation
  6. Download figures and tables

Snapshots

Version history

  • 2018-06-22 version 1.4
    • Version of Virus-Host DB: RefSeq release 88
  • 2018-04-24 version 1.3
    • Version of Virus-Host DB: RefSeq release 87
  • 2018-03-27 version 1.2
    • Version of Virus-Host DB: RefSeq release 86
    • New feature: gene annotaion method can be selected from prokaryotic, eukaryotic, and user defined genes.
    • Improved usability: the number of the max upload sequences is expanded to 50.
    • Improved usability: long sequence ID (up to 30 characters) is acceptable. Sequence IDs can include dots and hyphens.
    • Improved usability: Colors in alignment view can be customized.
  • 2017-02-08 version 1.1
    • Version of Virus-Host DB: RefSeq release 76
    • New feature: "related" proteomic tree is available in user sessions
  • 2017-01-04 version 1.0
    • Version of Virus-Host DB: RefSeq release 76
    • Initial release of ViPTree

Code availability

We developed ViPTreeGen, a command line tool for viral proteomic tree generation.

Reference virus data

Reference viral sequences and taxonomic information are available at Virus-Host DB.

Related work

We published a study of over thousand marine EVGs (environmental viral genomes). In the study, a prototype of the ViPTree server was developed and applied to the analysis.
Supplemental page for the study (including proteomic tree viewer and alignment viewer) can be browsed.

Citation

If you use results (data / figures) genereted by ViPTree in your research, please cite:
Following papers are related in methodological aspects to the ViPTree server.
  • Nishimura, Y. et al. Environmental viral genomes shed new light on virus–host interactions in the ocean.
  • mSphere, 2, e00359-16, doi:10.1128/mSphere.00359-16 (2017) [PubMed]
  • Bhunchoth, Y. et al. Two asian jumbo phages, ϕRSL2 and ϕRSF1, infect Ralstonia solanacearum and show common features of ϕKZ-related phages.
  • Virology, 494, 56-66, doi:10.1016/j.virol.2016.03.028 (2016).

Feedback

We appreciate bug reports, comments, and suggestions. The form is here.