Fig. 5

For each of 131 52 nt frameshift stimulating signals (FSS) from family RF00480 from the Rfam 12.0, RNAsampleCDS generated 100,000 RNAs that have the same slippery sequence as the Rfam sequence, and code 17-mer peptides p [resp. q] in reading frame 0 [resp. 1] each of whose amino acids has BLOSUM62 similarity of at least +1 with the corresponding amino acid in the Pol [resp. Gag] peptide coded by the Rfam sequence. Stem-loop formation probability, P([ ]), and stem-loop minimum free energy (MFE) were computed by RNAshapes [21] with the command RNAshapes -q -m ‘[]’. a Average stem-loop formation probability for 100,000 sequences sampled from RNAsampleCDS for each RF00480 sequence (red); stem-loop formation probability of HIV-1 frameshift stimulating signals from RF00480 (blue). Overall mean RNAsampleCDS samples is 69%±12 (red), while that for the RF00480 sequences is 99.3±2.2 (blue). b Average stem-loop MFE for 100,000 sequences sampled by RNAsampleCDS for each RF00480 sequence (red); stem-loop minimum free energy for HIV-1 frameshift stimulating signals from RF00480 (blue). Overall mean for RNAsampleCDS samples is 13.43±2.32 kcal/mol (red), while that for RF00480 sequences is −24.43±3.91 kcal/mol (blue)