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Genome Landscapes and Bacteriophage Codon Usage

Figure 1

GC3 and CAI landscapes for lambda phage.

Landscapes of GC3. (left) and CAI (right) measures of codon usage in Lambda phage. Only coding sequences are considered, which when concatenated together are 40,773 bp long (see Table 2). The GC3 landscape is the mean-centered cumulative sum of the GC3 content (GC3 = 1, AT3 = 0) of codons. The CAI landscape is the mean-centered cumulative sum of the log w-value for each codon. For each landscape, a region exhibiting an uphill slope corresponds to higher than average GC3 or CAI. The horizontal purple band represents the expected amount of variation in a random walk of GC3 or AT3 choices, given by Equation 2. Both landscapes exhibit features far outside of the purple bands, indicating that the patterns of codon usage are highly non-random. Gene boundaries are represented by the bars in the histograms below each landscape. The height of the bars in the histogram indicate the GC3 and CAI values for each gene.

Figure 1

doi: https://doi.org/10.1371/journal.pcbi.1000001.g001