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Genome Landscapes and Bacteriophage Codon Usage

Figure 3

Observed and randomized landscapes for lambda phage.

The figure shows the observed GC3 (left) and CAI (right) landscapes, plotted in black, along with the mean±1, and ±2 standard deviations of randomized trials, shown in aqua (bold line, dark and light regions, respectively). The aqua randomization test shown here draws random synonymous codons that preserve the exact amino acid sequence, according to probabilities that preserve the global codon usage distribution of the lambda genome. For the most part, the observed landscapes lie significantly outside the distribution of randomized landscapes–implying that the amino acid content of genes is not responsible for the observed pattern of the CAI landscape. In the lower panel, however, genes whose GC3 (left) or CAI (right) values fall between the 0.025 and 0.975 quantile of the random trials are shadowed in grey; the GC3/CAI values of such genes are not significantly different from random, given their amino acid sequence.

Figure 3

doi: https://doi.org/10.1371/journal.pcbi.1000001.g003