Table 1.

Comparison of the capabilities of existing methods designed to detect differential reactive nucleotides in rRNA molecules

Tool	Reference	Inter-replicate variability?	Noise considered?	Detection level?	False positives: 18S rRNA	False positives: 18S rRNA dataset 2
classSNitch	[28]	✗	✓	Regional	N/A	N/A
PARCEL	[29]	✓	✗	Regional	61	N/A
RASA	[30]	✓	✓	Regional	4	N/A
deltaSHAPE	[22]	✗	✓	Regional	97	16
StructDiff	[31]	✗	✓	Regional	N/A	N/A
dStruct	[32]	✓	✓	Regional	3	0
diffBUM-HMM	This work	✓	✓	Regional and Nucleotide	0	0

The table shows the previously published results of the analyses on the identically DMS-treated yeast rRNA datasets [27, 32] as well as the results from our diffBUM-HMM analysis of these datasets. The column displaying the number of false positives indicates the number of nucleotides that were called differentially modified in DMS chemical probing data