Viral Bioinformatics Research Centre

Chris Upton, University of Victoria, Canada

Poxviridae

Poxviridae

The Poxviridae has two subfamilies: Chordopoxvirinae, poxviruses of vertebrates, and Entomopoxvirinae, poxviruses of invertebrates. The genome is a linear dsDNA molecule with of 130-375 kb; it contains inverted terminal repeated sequences which are covalently cross-linked at the end. Poxviruses replicate in the cytoplasm of infected cells and encode their own complex transcription system. Many poxvirus genes are not required for replication in tissue culture, but function to inhibit anti-viral processes of the host.

 

Poxviruses and the VBRC

The VBRC provides comprehensive web-based genomics resources to the scientific community through: 
  • Providing up-to-date genomic and proteomic data from the virus families.
    • see Organisms menu for a list of virus families supported
  • Providing easy-to-use software tools to perform a variety of bioinformatics analyses.
    • see Tools menu for a list of software tools
    • we also build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists.
  • Offering researchers help on specific bioinformatics problems.

You can find the VBRC’s mandate here and more information on the home page.

Analysis tools at the VBRC

We provide highly interactive software tools that enable users to view and analyze viral genomes. These tools can be accessed directly from the “Poxviridae Tools” drop-down menu on the top left of this page. These tools include:
  • Viral Orthologous Clusters (VOCs) allows users to easily search the Poxviridae database for protein sequences or genes of a known function or of a specific genome and then apply different analysis techniques to the search result. VOCs provides quick and easy access to tools like BLAST, multiple alignment, dotplots, and genome statistics.
  • Viral Genome Organizer (VGO) allows users to browse genomes, viewing genes, ORFs, start/stop codons, nucleic acid composition, and orthologs when working with multiple genomes.

To start work: Check the Quick Start Tutorials (well worth 5 minutes) or just dive in by selecting a tool from the menu. Our usual starting place is the VOCs, which allows you to select data for use with the analysis tools.

Poxvirus information

The VBRC provides a Poxvirus Information Book that includes:

  • Up-to-date website links to collections of published research reviews through NCBI.
  • Links to other poxvirus internet resources for general and background information.

Follow  @pox_papers  on Twitter to see what is being published about poxviruses.

Genomes excluded from VOCs

  • MF661791.1: Eastern grey kangaroopox virus strain NSW (Misassembly lead to false claims of recombinations; reassembled MF661791.2 nearly identical to EKPV-SC)

Problematic Genomes included in VOCs

  • LT993226: Cowpox virus Ger/2014/Human (Crucial RPO genes J6, A24 are fragmented, RPO gene J4 is truncated)
  • KY569020: Cowpox virus CheNuru_DK_2012 (Crucial RPO genes G5.5R, J6R are truncated)
  • KY549146: Cowpox virus K779 (Missing ChPV conserved genes such as J1, D4 etc)
  • KY549147: Cowpox virus K780 (Missing ChPV conserved genes such as J1, D4 etc)