Table 1.

Recovery of helices across seven complex RNA folds from M2-seq data

RNA	No. of helices*	ShapeKnots + DMS + M2†		M2-net
		TP	FP	TP	FP
P4–P6 domain	8	8	1	7	0
GIR1 ribozyme	11	11	0	5	0
RNase P C domain	13	11	1	10	1
AdoCbl riboswitch	10	10	0	4	0
ydaO riboswitch	7	6	1	2	0
Zika xrRNA	5	4	1	2	0
TPP riboswitch	6	6	0	3	0
Total	60	56	4	33	1
False-negative rate, %		6.7		45.0
False-positive rate, %		6.7		2.9
Sensitivity, %		93.3		55.0
PPV, %		93.3		97.1

FP, false positives; PPV, positive predictive value; TP, true positives.

^*Helices with length greater than two Watson–Crick (or G•U wobble) base pairs.

^†Use of one-dimensional DMS data to guide folding through energy bonuses (5) and Z-scores derived from 2D M2-seq experiments, applied as in ref. 16.