Fig. 4.—

Predicted effect of transition mutations and non-synonymous mutations in the FMDV genome and 3D-coding region. (A) Fraction of non-synonymous mutations for each transition in the 3D-coding region and the entire FMDV genome; statistical significances are given in the text. (B) Mean change in folding free energy (ΔΔG; negative values correspond to stabilizing substitutions) resulting from all possible non-synonymous transitions in the 3D-coding region, as predicted by PoPMuSiC and DeltaGREM. Both programs agree qualitatively on the comparison between different transitions, although DeltaGREM tends to predict more mutations as being stabilizing (ΔΔG < 0). Procedures are detailed in Materials and Methods.