The relationship between codon usage and protein function in lambda phage.
The figure shows the aqua (CAI, as in Figure 3) and orange (BCAI, as in Figure 5) randomization tests overlaid with information about protein function: genes classified as structural are shown with a white background and all other genes with a grey background. The histograms indicate a clear relationship between the structural classification of a gene and its significance under the aqua and orange tests: structural genes typically have elevated quantiles in the aqua test, whereas other genes typically have depressed quantiles. In other words, structural genes exhibit elevated CAI values when controlling for their amino acid sequence, compared to codon usage in the genome as a whole. Moreover, as the orange histograms indicate, this pattern is not caused by variation in GC3 content: the structural genes exhibit elevated BCAI values after controlling for both their amino acid sequence and their GC3 sequence.