Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses
Fig 5
Predicted stem-loop in M vRNA in the region corresponding to M1 codons 65–72.
The image shows a truncation to the region of interest (nucleotides corresponding to codons 65 and 72 marked) of the RNAalifold prediction of the constrained region arising from RNAdescent analysis of H5N8 avian host sequences, using raw (unranked) constraint data. All RNAdescent analyses, except those of H1N1 human host sequences with ranked constraint data and H3N2 human host sequences with raw constraint data, predict constraint in this region and the base pairings displayed here are replicated in all other RNAalifold predictions. (Some RNAalifold analyses predict one or two additional base pairings that elongate the stem.) Base pairs are highlighted by RNAalifold in deep red when all sequences are capable of forming the pairs shown. Base pairs are highlighted in deep yellow when all sequences are capable of forming the pair shown or one other pair (including GU pairs). RNAalifold was used with input options disallowing lonely pairs, allowing G-quadruplexes, and with the ribosum scoring matrix enabled. Avian strain folds were produced with the temperature set to 41°C.