Codon Usage

This analysis requires both allelic profiles and the allele sequences to be loaded.  Again, individual isolates may be selected or deselected from inclusion using the 'Isolate Selection' dialog reachable from the 'Options' menu.  This analysis also requires that the open reading frames are identified for each locus and the program will prompt for this information.  If necessary, it will take you to the 'Reading Frames' dialog where these can be auto-detected.

To run the analysis, click 'Analysis ... Data Summary ... Codon Usage'.  This will then count the codons used across all loci and the selected strains.  Output is in the form of a table showing the number of occurrences of each codon, the proportion per 1000 codons, % occurrences per synonymous codon family and the relative synonymous codon usage.

Program Output

Amino Acid Codon Number of occurrences Occurrence per 1000 codons % Occurrences per synonymous codon family Relative Synonymous Codon Usage (RSCUi)
Gly GGG 62 0.4 0.4 0.017
Gly GGA 815 4.8 5.6 0.225
Gly GGT 4030 23.6 27.8 1.111
Gly GGC 9606 56.3 66.2 2.648
Glu GAG 1836 10.8 13.6 0.272
Glu GAA 11642 68.2 86.4 1.728
Asp GAT 3800 22.3 34.1 0.682
Asp GAC 7349 43.1 65.9 1.318
Val GTG 4350 25.5 33.3 1.332
Val GTA 967 5.7 7.4 0.296
Val GTT 3788 22.2 29.0 1.160
Val GTC 3957 23.2 30.3 1.212

... continues for all codons