Table 9.8.
Illustration of CAI calculation for a gene whose observed codon frequencies are in column “ObsFreq”
| Codon | AA | ObsFreq | RefCodFreq | w |
|---|---|---|---|---|
| GCA | A | 1 | 195 | 0.606 |
| GCU | A | 15 | 322 | 1.000 |
| GCG | A | 0 | 81 | 0.252 |
| GCC | A | 8 | 242 | 0.752 |
| UGC | C | 3 | 123 | 1.000 |
| UGU | C | 3 | 112 | 0.911 |
| GAU | D | 9 | 69 | 1.000 |
| GAC | D | 11 | 40 | 0.580 |
| GAG | E | 11 | 289 | 0.863 |
| GAA | E | 14 | 335 | 1.000 |
| UUU | F | 3 | 118 | 0.554 |
| UUC | F | 9 | 213 | 1.000 |
| … | … | … | … |
The codon frequency of the highly expressed reference set is in column “RefCodFreq.” The column “w” is obtained by dividing RefCodFreq values by the largest value in the codon family