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Fig. 2 | Genome Biology

Fig. 2

From: diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data

Fig. 2

diffBUM-HMM effectively detects differentially reactive nucleotides in the earliest detectable yeast pre-rRNA precursor. A The top panel shows the SHAPE reactivities [33] from the first biological replicate of both wild-type Mrd1 and Mrd1 Δ5 deletion mutant, which were used to identify DRNs with deltaSHAPE. The deltaSHAPE values were calculated according to [22]. For the deltaSHAPE panel, positive values indicate the position of nucleotides that are more reactive in pre-rRNA associated with wild-type Mrd1, whereas negative values indicate the position of nucleotides that are more reactive in pre-rRNA associated with the Mrd1 Δ5 mutant. The same data was reanalyzed using the diffBUM-HMM and dStruct algorithms (panels 4 and 5, respectively). For the diffBUM-HMM results, the posterior probabilities for differential states 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]. B The same as in A but only for the 5 ETS and 5 end of 18S rRNA. We additionally included the results from the PE analysis (panel 2). The gray areas indicate the regions validated by PE analysis

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