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. 2010 Oct 5;5(10):e13171. doi: 10.1371/journal.pone.0013171

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Nunes et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) Ratio between the amino acid ‘expected’ frequency (calculated by mathematical modeling using two different overall mean R values, 1.2 (upper row) and 3.6 (lower row) – see methods) and the ‘observed’ frequency for the 251 genetic variants. Normalized ratio intervals (log2) are color-coded. For Trp, which was the unique amino acid that was never created from the total 511 variable sites found in ompA, the ‘observed’ frequency was calculated by determining the mid-point of the respective exact 95% confidence interval using the ration between the F and Binomial distribution [57]. (B) Empirical data showing the ratio of created/removed amino acid substitutions that were ‘observed’ among the 251 genetic variants. Normalized ratio intervals (log2) are color-coded, and each amino acid is shown below to the correspondent interval. Statistical significance (P≤0.02) was found for the amino acids marked with an asterisk. For panels (A) and (B), logarithmic transformation of the ratios is required for symmetrical distribution of the data around zero.