Instructions for use of VirusCodon software
VirusCodon has 4 pages that are used to help select the sequences and features for analysis.
- Click the Get Genera button to retrieve the complete list of genera in the database. Genera are colour coded to help identify those whose members infect plants, fungi etc. (see the About… Genera colour codes… menu).
- Select a genus from the left hand column (using the left mouse button) and use the Get Viruses button used to display the members. This will be the complete list of recognised and tentative members of the genus (there will not be sequences associated with all of them).
- Select the virus of interest (using the left mouse button) and click on the Get Accnos button.
Accnos: This page lists all the available accessions of the virus previously selected with
a brief description of each. Select one or more sequences using the buttons or the check boxes and
click on the Get Features button.
Features: This page lists all the features detected in the sequences selected.
Choose one or more features using the check boxes and click on the Get Codons button.
Codons: This page provides the output. The level of detail displayed can be controlled using the Display menu.
- If Seq Codons is checked, the display will include the complete codon table for each feature that has been selected.
- If Total Codons is checked, the display will include the codon table for all the selected features combined.
- The display will always include a summary table that provides for each selected feature and for the total of all features, the Gene name, the accession number, the number of codons, the total %GC, the GC% for each codon position and the ENC (Effective Number of Codons), which is a simple overall measure of bias in synonymous codon use (Wright, 1990, Gene 87, 23-29).
The output on this page is in tab-delimited format and can be copied by clicking and dragging the mouse and using standard Windows Ctrl+C to copy to the clipboard. It can then be pasted into another application. There is also a button to Clear
the display, if required, before selecting another virus for analysis.