Fig. 3

diffBUM-HMM detects differentially reactive nucleotides (DRNs) in the 5 ^′ ETS of the 35S pre-rRNA precursor. A, B SHAPE reactivities, deltaSHAPE, diffBUM-HMM, and dStruct analysis results for two regions (positions 268–352 and 405–502) within the 5 ^′ ETS. The top panel shows the SHAPE reactivities [33] from the first biological replicate, which were used to identify DRNs with deltaSHAPE (deltaSHAPE panel). Positive values indicate the 1M7 nucleotide reactivities in pre-rRNA associated with wild-type Mrd1, whereas negative values indicate the reactivities in pre-rRNA associated with the Mrd1 deletion (Δ5) mutant. The second panel shows the quantification of the PE analysis for these regions. The same data was reanalyzed using the diffBUM-HMM and dStruct algorithms (panels 3 and 4, respectively). For the diffBUM-HMM results, the posterior probabilites for differential reactivity were calculated using the raw counts. For the dStruct analyses, 2–8% normalized RT drop-off rates were used, as recommended by the authors [32]