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 2
Folds of PB1 3′ vRNA regions whose cRNA is deemed conserved by RNAdescent.
A small conserved stem-loop can be seen. Labels correspond to the influenza A subtype, host, and analysis method (raw constraint data or ranked constraint data) that predicted the constrained region. Folds are of the (− sense) vRNA, produced using RNAalifold. The folds displayed are truncated to the regions containing information on the stem-loop we discuss, using base pair predictions from the folds of the full regions predicted to be constrained; the full region folds may be found in S4 and S8 Figs. The folds are annotated with PB1 codon 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. Avian strain folds were produced with the temperature set to 41°C.