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