Viral Orthologous Clusters


NOTE: At this time VOCS can only be used on your system if you are running the latest Java Runtime Environment. Download it here:  Java Runtime Environment 1.7.
Viral Orthologous Clusters (VOCs) is an easy-to-use Java GUI used to access the VBRC genome databases. With this program, you can:

  • Search and extract genome, gene and protein data from the database.
  • Select data (e.g. a set of genes) and then analyze it with the other VBRC tools, e.g.
    • Generate multiple alignments with Base-By-Base
    • Create dotplots with JDotter
    • Browse complete genomes with the Viral Genome Organizer (VGO)
    • Run BLAST searches on NCBI and VBRC databases
    • Plot DNA skews with DNAGrapher
    • Create genome maps
  • Compare genomes and sets of genomes, e.g.
    • find gene families represented in all poxvirus genomes (core poxvirus genes)
    • find gene families present in variola viruses, but not in cowpox or vaccinia viruses (potential virulence genes)
  • Our current databases include Adenoviridae, Asfarviridae, Baculoviridae, Coronaviridae, Herpesviridae, Iridoviridae, and Poxviridae. If you would like us to add any genomes or inquire about creating a new database, please contact us using the link at the bottom of the page.
  • The VBRC uses an Administrator version of VOCs to add genomes, annotate genes and classify gene families

 


Getting Started


If you’re new to VOCs, click on the launch button (on the right) and use the Quick Start Page to learn the basics (or if you’re like us…  just start clicking!).

The VBRC also provides additional help resources for VOCs:

 


References


If you use this resource please cite the relevant papers (publication list).

Ehlers, A., J. Osborne, Slack, S., R. L. Roper, and C. Upton. 2002.

Poxvirus Orthologous Clusters (POCs). Bioinformatics 18, 1544-1545

Upton, C., Slack, S., Hunter, A.W., Ehlers, A. and R. L. Roper. 2003.

Poxvirus Orthologous Clusters (POCs): Toward defining the minimum essential poxvirus genome. J. Virology, 77, 7590-7600.

Papers which have cited VOCs

 


Troubleshooting


At this time Viral Orthologous Clusters will only launch if you are running the latest version of Java on your system. Download it here:  Java Runtime Environment 1.7. Please see Java Web Start Setup and Java Web Start Tips for help.

 


Submit a feature request


Is there a feature that you think this tool needs? Submit a wish.

 

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