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 3
Representative fold of stem-loop in PA 3′ vRNA region whose cRNA is deemed constrained by RNAdescent.
The fold displayed is of H7N9 avian host sequences, truncated to a region covering NC_026424.1 nucleotides 23–46, using base pair predictions from the folds of the full regions predicted to be constrained. The nucleotides corresponding to codons 9 and 15 are labelled. RNAalifold predicts similar folds for multiple analogous constrained regions in other subtype/host/RNAdescent analysis type combinations (S2, S6, S7 and S8 Figs), and one slightly differing fold in one analogue (S4 Fig). The displayed fold is of the−sense vRNA, produced using RNAalifold [17, 18]. 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/mid yellow when all/all but one 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.