Relative frequency of A3G/F hotspot motifs inside <i>vs.</i> outside CTL epitopes in HIV genes.

<p><b>A.</b> For each HIV gene, the frequency of A3G/F hotspots (either all hotspots: GGG, GGA, GGT, GAA, or GGG alone) was calculated in genomic sequences that encode CTL epitopes and sequences that do not encode for CTL epitopes. Normalized frequencies were calculated by taking into account the total nucleotide length of the sequence. For each HIV gene, the normalized frequency of A3G/F hotspots inside sequences that encode CTL motifs was divided by the normalized frequency of A3G/F hotspots in sequences that do not encode CTL epitopes to generate a Ratio (R-value). The average of R-values amongst all HIV genes was determined and each R-value was divided by the average to obtain the index value, which reflects enrichment of hotspots within CTL epitopes, relative to other HIV genes. <b>B.</b> The same analysis as panel A was conducted within each HIV gene to compare the relative enrichment of A3G/F hotspots in sequences that encode CTL epitopes restricted to different HLA alleles. <b>C.</b> Comparison of A3G/F enrichment in CTL epitopes <i>vs.</i> the portions of the Env gene that encode antibody recognition epitopes. Average R-value for the CTL epitopes of all genes (average of all R values from panel A) was compared to the R value of A3G/F hotspots inside/outside sequences encoding antibody recognition motifs within Env. Index value of 1 is shown as a scale because an index >1 indicates relative enrichment.