Summary of conserved local base-pairing interactions in HIV-1 PR and RT wild-type consensus sequences

Mfold analysis was carried out using a sliding window scanning process (implemented in perl) to minimize any arbitrary effects of the region chosen for analysis. Stepwise scanning in a 5’ to 3’ direction with a ‘sliding window’ of fixed length was used to generate subsequences within the region of the HIV genome under analysis (codons 1-99 of PR and 1-240 of RT) and 500bp of flanking sequence either side (derived from subtype consensus sequences available from the Los Alamos HIV Sequence database).

A step size of 20bp was used in combination with a range of window sizes (300, 600, 900 and 1200bp). Base pairing interactions within predicted structures generated using this approach were then analysed. The frequency of base-paring between pairs was calculated across each of the windows in which the pair occurred.