Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA
Fig 2
Representative global sequence alignment between E. coli and C. difficile 16S ribosomal RNAs using model-free SHAPE reactivities as the only constraint.
Alignment is shown as a function of E. coli sequence numbering. (A) Alignment of SHAPE reactivities across a 250-nucleotide window. (B) A 60-nucleotide subsection of this alignment, including primary sequences. Areas of sequence identity are emphasized in bold.