Open Codon Statistics. Select the virus family of interest from the list that appears. Another window will open containing a list of viruses in the family; click on the virus of interest. (NOTE: you can only select one virus at a time.)
A console window with a list of virus genes will appear. Select the gene(s) of interest, then go to the View Data menu; choose “View Selections.” A chart of codon statistics will open containing data for the selected genes.
– The top half of the chart shows gene-by-gene codon position data, as a percentage of all nucleotides in the gene (e.g. A in position 1 = 12.77%).
– The bottom half of the chart shows statistical data averaged over all selected genes.
Further data is available from the View Nucleotide Distribution menu. Choose the nucleotide of interest (e.g. G.) A window will open containing (top half) G-specific data for each gene in the table, and (bottom half) G-specific stats averaged over all genes.
To view codon statistics over an entire genome, open the genome of interest. When the list of genes appears, select “View All” from the View Data menu. The top half of the table, as before, is a gene-by-gene breakdown of codon statistics; the bottom half gives codon statistics averaged over all genes in a genome. (Note that only predicted coding regions are analyzed; non-coding regions are excluded from these statistics!)
Codon Statistics allows you to export table data to tab-delimited plain text files. Simply choose “Save As” from the File menu; enter the file location and name. A plain text file containing all codon statistics currently displayed will be created.
To obtain a graph of codon data, select the gene(s) of interest. Go to the Graph menu and select the desired graph type. Bar and line plots grouped by nucleotide or intracodon position (1, 2, or 3) are available.
– If you select a single gene, a single graph will be displayed with its data.
– If you select multiple genes, only a single graph will again be displayed and will contain average values over the genes selected.
– To obtain individual graphs for several genes, select them one at a time and choose the desired graph from the Graphmenu.