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Table 1 Comparison of the capabilities of existing methods designed to detect differential reactive nucleotides in rRNA molecules

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

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
  1. 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