Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies

Mustonen and Lässig et al. 10.1073/pnas.0505537102.

Supporting Information

Files in this Data Supplement:

Supporting Text
Supporting Figure 5
Supporting Figure 6
Supporting Figure 7

Supporting Figure 5

Fig. 5. Detection error trade-off for CRP binding site prediction. Expected rates of false positives vs. false negatives for a single-species search with position weight scoring in E. coli (1), a two-species search including S. typhimurium (2), and a three-species search including also Y. pseudotuberculosis (3). The diamonds indicate the points r_Q= 0.30, used as lower cutoff in our prediction lists.

Supporting Figure 6

Fig. 6. Dot plot of energies for three species comparisons. E₁, E₂, and E₃ refer to E. coli, S. typhimurium, and Y. pseudotuberculosis, respectively.

Supporting Figure 7

Fig. 7. Functional phylogenies for three species. Example of the R^t_00s(E₁,E₂,E₃) ensemble. Green arrows denote the switching point. Blue lines mark the neutral evolution of nonfunctional loci (G^t₀) and red evolution under selection (G^t_s).