Viral Genome Organizer


Viral Genome Organizer (VGO) is an easy-to-use Java genome browser.  It can be used to display information about a genome, including its genes, ORFs and start/stop codons. It can also be used to perform a regular expression search, a fuzzy motif search, and a masslist search. Because VGO talks to our database of genome sequences (VOCs) it can be used to compare genomes.

With this program, you can:

  • view genes and predicted ORFs in one or a series of genomes.
  • display start and stop codons within the sequence
  • search for sequences within genomes
    • using regular expressions; e.g  GGATCC  or  TTTTT[ATCG]T
    • using a fuzzy search pattern; e.g.  GGATCC allowing one mismatch
    • for genes with the highest AT composition
  • use a GUI to select and extract regions of a genome
  • display orthologs in a set of genomes by using the GUI to select a gene in another genome
  • display a plot of nucleotide composition.
  • search for the longest oligonucleotide shared between a series of unaligned genomes
  • search the translated genome for matches to mass spec peptides
  • graphically display data from other programs on top of the genome display

Please note that Java has enhanced security on all web applications and is now requiring all apps to be signed by a certificate from a trusted authority. We are currently updating all of our apps to a new certificate and in the mean time are using a self-signed certificate. Any application with a self-signed certificate is blocked by default on your computer unless your Java Security Settings are set to ‘Medium’ or our URL is added to the Exception Site List. There may also a pop-up window on start up of the app where you will have to accept the risks regarding the certificate. Please bear with us as we fix this!

For instructions on how to add our URL to the Exception Site List and more information regarding the new security settings look here:

https://www.java.com/en/download/help/java_blocked.xml



Getting Started


If you’re new to VGO, 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 VGO:

 

 


References


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

Lefkowitz, E. J., Upton, C., Changayil, S. S., Buck, C., Traktman, P., Buller, R. M. L. 2005. 
Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource. Nucleic Acids Res. 2005 33: p. D311-D316

C. Upton, D. Hogg, D. Perrin, M. Boone and N. Harris, 2001.
Viral Genome Organizer: A system for analyzing complete viral genomes. Virus Research 70, 55-64.

Papers which have cited VGO

 


Troubleshooting


If your system does not launch Viral Orthologous Clusters, it is probably missing Java Runtime Environment 1.5. 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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