Evidence of Divergent Amino Acid Usage in Comparative Analyses of R5- and X4-Associated HIV-1 Vpr Sequences

Figure 3

Jensen-Shannon divergence identifies positions with differential amino acid profiles between R5 and X4 Vpr sequences. The Jensen-Shannon divergence between R5 and X4 Vpr sequences was computed for each amino acid position and plotted with a black circle. Statistically divergent positions, as determined by a one-tailed Monte Carlo permutation test (1000 iterations), are indicated by a red star (). This methodology was repeated for each of the reduced alphabets, Murphy-15, Murphy-10, Murphy-8, and Murphy-4.