CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	NanoFolder		RDfolder
MCC	0.626	>	0.528
Average MCC ± 95% Confidence Intervals	0.745 ± 0.228	>	0.635 ± 0.340
Sensitivity	0.680	>	0.492
Positive Predictive Value	0.597	>	0.594
Total TP	83	>	60
Total TN	3980	<	4018
Total FP	60	>	42
Total FP CONTRA	15	>	6
Total FP INCONS	41	>	35
Total FP COMP	4	>	1
Total FN	39	<	62
P-value	0.0

Comparison of performance of NanoFolder and RDfolder. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for NanoFolder and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for NanoFolder and RDfolder. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for NanoFolder and RDfolder).

Total Scores
MCC	0.626
Average MCC ± 95% Confidence Intervals	0.745 ± 0.228
Sensitivity	0.680
Positive Predictive Value	0.597
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.54	0.61	0.50	11	506	11	1	10	0	7
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
3J16_L	tRNA links to Rfam database...	0.43	0.52	0.37	11	1129	19	8	11	0	10
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.39	0.41	0.39	12	1406	20	4	15	1	17
4ENC_A	crcB links to Rfam database...	0.66	0.73	0.61	11	478	9	2	5	2	4

Total Scores
MCC	0.528
Average MCC ± 95% Confidence Intervals	0.635 ± 0.340
Sensitivity	0.492
Positive Predictive Value	0.594
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	514	14	3	11	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
3J16_L	tRNA links to Rfam database...	0.26	0.24	0.31	5	1143	11	0	11	0	16
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.