Viral Orthologous Clusters
Jan 2020: If VOCs doesn’t launch – re-download the JNLP file.
NOTE: Java 8 is recommended. Do not use Java 11. Download it here: Java Runtime Environment.
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.
- Our current databases include Asfarviridae, Baculoviridae, 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.
- 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)
- 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
- The VBRC uses an Administrator version of VOCs to add genomes, annotate genes and classify gene families
- NEW FEATURE: Jan 2017
- You can now easily concatenate a series of genes/proteins from multiple genomes to create a multiple sequence alignment using a set of orthologs (e.g. 10 proteins from 10 viruses).
- Select genomes, click OrtGrpView button
- Select orthologs, click Analysis menu to select whether to concatenate the genes or proteins
- Results open in Base-By-Base. Note: blocks of XXXs separate the gene/protein sequences. Align sequences in Base-By-Base.
- You can now easily concatenate a series of genes/proteins from multiple genomes to create a multiple sequence alignment using a set of orthologs (e.g. 10 proteins from 10 viruses).
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:
- How to doc; short descriptions of certain analyses you might want to do.
- VBRC Help Book, which is our comprehensive reference manuals.
- FAQs (Frequently Asked Questions)
- Finally, just email us a question and we’ll gladly help you out.
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
Java 8 is recommended. Do not use Java 11. Please see Java Web Start Setup and Java Web Start Tips for help.
