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Genome Landscapes and Bacteriophage Codon Usage

Figure 7

Green (left) and orange (right) randomization tests for several phages.

Bacteriophages P2 (A) and T3 (B) both infect E. coli. Phage D3112 (C) infects P. aeruginosa. Phage bIL286 (D) infects L. lactis. T3 is the only non-temperate phage of this group. See Table 2 for combined Fisher p-values for these tests. In the case of bIL286, note the lack of evidence for codon bias evident in the green and orange tests for bIL286, as confirmed by the insignificant p-values in Table 2. In this case, we cannot rule out the possibility that the observed pattern in GC3 is determined completely by the amino acid and CAI sequence (green), or that the observed pattern in CAI is determined by the amino acid and GC3 sequence (orange).

Figure 7

doi: https://doi.org/10.1371/journal.pcbi.1000001.g007