Figure 4.

Pairing predictions along the polio reference sequence. RNA-Decoder, Pfold and RNAalifold were used on the polio alignment and the pairing probabilities for the alignment were then projected onto the reference sequence. Mfold was directly used on the reference sequence. Please refer to the text for more information on how the scan of the polio genome was performed. The protein-coding region starts at position 1 and ends at position 6639 (i.e. the stop codon is at positions 6640–6642). We have only been able to recover precise annotations of a single experimentally verified RNA structure from the literature (46). However, several elements have been inferred by homology to other vira and analysis of compensatory mutations in both the 5′UTR and the 3′UTR [(48) and references therein].