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We would like to explain why we make emphasis on minimal contrast and not on mutation bias, when presenting Table 2.
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i are the numbers of codons ending with U or C, respectively, in codon family i, and BC→T is a constant representing C→T mutation bias (being 0.5 when there is no C→T mutation bias).
That is, selection will cause a correlation between ENC and CAI, but the randomness of mutation will lessen this correlation when mutation bias becomes a relatively stronger force.
The dotted line in each graph in Figure 7 are for completely equal usage of all codons, when mutation bias to A/T is exactly balanced by selection to G/C; thus one interpretation is that genes to the left of the dotted lines are dominated by mutation while those to the right are dominated by selection.
Genes/amino acids with completely even codon usage would occur only when the mutation bias toward A/T is exactly balanced by selection toward G/C.
When the mutation bias favors GC, the normalized energy gap tend to be higher than the threshold and the unfolding free energy tend to be small.
The contrary holds when the mutation bias favors GC-poor codons: In this case β i is large, and the site experiences strong purifying selection.
Mutation bias can affect codon usage especially when selection is weak.
If our hypothesis for the detection of genes important for pathogenesis is correct, then we should expect that a mutation bias would generally span entire operons when the corresponding genes participate to the process of pathogenicity.
But when selection is weak, mutation bias towards loss of function can affect evolution.
Therefore, it will be necessary to consider potential for bias when individuals are screened for mutations on the basis of their tumor phenotype.
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