Fig. 4.

The advantage of transitions implied by various biochemical factors. The 245 biochemical factors from AAindex were used to compute a pairwise similarity measure for amino acids indicating their biochemical similarity, then these measures were used to assess whether transitions are more conservative than transversions. AUC is the chance that a replacement due to a transition has a higher similarity score than a randomly chosen transversion (where the random sampling of transitions and transversions is based on the pool of actual mutants from the eight studies). The resulting distribution indicates that transitions are more conservative according to about 3/5 of biochemical factors (AUC > 0.5), and less conservative according to the other 2/5 of factors (AUC < 0.5).