Figure 1

Map of the HIV-1 genome. For clarity, the genome is represented as linear, with the genes represented as a concatemer (top bar). The following layers of data are shown: Conservation: black = amino acid conservation less than 95%. RNA: dark blue = extensively structured RNA (SHAPE parameter < 0.25), light purple = flexible RNA (SHAPE > 0.5). Protein structure: blue = structured (β-sheet or α-helix), grey = no structural information available for vif, vpr, tat, rev, vpu and nef. Overlapping region: green = sites in overlapping reading frames. Positive selection: dark purple = sites under positive selection. CD8 T cell epitope: pink = CD8 T cell epitope, CD4 T cell epitope: light pink = CD4 T cell epitope, AB epitope : red = antibody epitope, AA and AG enrichment: orange = regions enriched in AA and AG dinucleotide motives.