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 9
RNAalifold structure prediction of the conserved stem-loops near the HA cleavage site in H7N9 human host viruses.
Nucleotide numbering follows RefSeq NC_026425.1 (GenBank KF021597.1). RNAalifold [18] uses a minimum free energy algorithm, modified to take into account how many sequences in an alignment can form predicted base pairs. Red (light red, pink)/yellow (light yellow, pale yellow) highlighted base pairs indicate that all (all but one, all but two) sequences in the alignment can form the base pair, with no/one alternative base pairing. We reproduce the small previously predicted [28] stem-loop starting at nt1030; although we predict a larger stem-loop near the cleavage site, it differs from stem-loops predicted for other strains.