Table 3.

Sensitivity and positive predictive values for secondary structure models predicted for the HIV-1 genome. Here the reference structure is the secondary structure reported for HIV-1 genome reported by Watts et. al. (2009). Method names for ScanFold refer to the window size used in parentheses, and for RNAfold, the max bp span used is in parentheses. For scoring, the HIV-1 genome reference structure was generated using the secondary structure reported in Watts et. al 2009. Predicted structures from RNAfold were generated using three different settings: (1) the MFE fold predicted for the entire genome [RNAfold] (2) the MFE fold for a max bp span of 120 nt [RNAfold(120nt)]and (3) an MFE fold using a max bp span of 600 nt [RNAfold(600nt)] (the setting used for the original modelling). The scanFold predicted structures (for windows sizes 100 to 210 nt) were taken directly from the supplemental CT files of Andrews et. al. 2018, here step sizes were 1 nt, randomizations were 50, and shuffling was mononucleotide; an additional prediction was performed using a window size of 600 nt directly on the webserver (step size of 1 nt and 50 randomizations). The sensitivity and positive predictive value (PPV) for each of the predicted secondary structures was calculated using the RNAstructure package’s scorer program (using exact enforcement).

	PPV (HIV-1)			Sensitivity (HIV-1)
Method	Total	Zavg < −1	Zavg < −2	Total	Zavg < −1	Zavg < −2
ScanFold(100nt)	0.325	0.529	0.795	0.284	0.2	0.111
ScanFold(120nt)	0.319	0.531	0.784	0.287	0.206	0.121
ScanFold(150nt)	0.323	0.500	0.682	0.279	0.218	0.12
ScanFold(180nt)	0.322	0.474	0.602	0.292	0.23	0.114
ScanFold(210nt)	0.349	0.495	0.607	0.315	0.246	0.124
ScanFold(600nt)	0.428	0.456	0.498	0.426	0.317	0.236
RNAfold(120nt)	0.304			0.392
RNAfold(600nt)	0.361			0.493
RNAfold	0.301			0.416