33% of mutations were synonymous and showed evidence of selection on codon usage.
All three were predicted to be low expressed based on codon usage by the PLS model.
The strand-biased mutation spectrum has profound consequences on codon usage in mitochondrial protein-coding sequences (CDSs) and the anticodon of tRNA genes [17].
Motivated by some unexpected observation on codon usage, we have developed a codon usage model based on GC-biased synonymous point mutations.
Thus the influence of GC bias on codon usage appears to be felt most strongly at the level of codon classes rather than the level of individual codons.
Finally, selection on codon usage and functional noncoding DNA could have contributed to reducing silent diversity.
These results are nothing but the superimposition of amino acid bias on codon usage bias.
It appears that nucleotide composition bias has a significant influence on codon usage.
Another common technique for genome classification is based on codon usage frequencies [ 43].
Our conclusion on the estimation of ω was therefore robust to assumptions on codon usage bias.
The effect of natural selection on codon usage quantifies the level of gene expression.
