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 4
Constraint analysis of PA 3′ cRNA (5′ vRNA) region.
Top: Examples of RNAdescent analysis output, for unweighted (raw) constraint data for H5N1 avian host sequences and for weighted constraint data for H7N9 human host sequences. Each point corresponds to one codon in PA, ordered 5′ to 3′ in cRNA. Codons that do not yield any information (weight zero) are plotted with open triangles. Orange points correspond to codons in regions deemed significantly constrained by the algorithm. In both cases, a steep descent can be seen in the centre of the plot corresponding to the conserved PA/PA-X out of frame overlap. A steep descent can also be seen to the 3′ side of the plot, indicating the long constrained regions found. Constraint is apparent throughout the entire regions. Bottom: Fold of (− sense) vRNA, from RNAalifold analysis of H5N8 avian host sequences. The region folded is the region of interest found in the 3′ cRNA from analysing ranked codon constraint data. To the right of the figure, a stem-loop corresponding to codons 685–689 may be seen. To the left of the figure, a stem-loop corresponding to codons 701–704 may be seen. The fold is of the−sense vRNA, produced using RNAalifold. Selected nucleotides are numbered with corresponding amino acid numbers. 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. The fold was produced with the temperature set to 41°C.