Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA
Fig 5
Consensus alternate structures in the decoding site.
Helices 28 and 44 of the E. coli 16S rRNA are shown. (A) SHAPE reactivities for aligned regions. Consensus base pairs are highlighted in gray. (B) Structures for the covariation and SHAPE-structure constrained models. Base pairs in the RNAalifold consensus are shown in black, and base pairs predicted in the follow-up constrained RNAfold prediction are gray.