Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA
Fig 4
Consensus alternate structures for helix 36 of E. coli 16S rRNA.
(A) SHAPE reactivities for aligned regions with consensus areas (RNAalifold) highlighted in gray. (B) Structures for the covariation and SHAPE-structure constrained models. Base pairs predicted in the first-step (RNAalifold) consensus are black, and base pairs predicted in the follow-up constrained (RNAfold) prediction are shown in gray.