CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	NanoFolder		RDfolder
MCC	0.483	>	0.470
Average MCC ± 95% Confidence Intervals	0.543 ± 0.189	>	0.515 ± 0.306
Sensitivity	0.558	>	0.435
Positive Predictive Value	0.440	<	0.531
Total TP	77	>	60
Total TN	6085	<	6147
Total FP	102	>	54
Total FP CONTRA	27	>	11
Total FP INCONS	71	>	42
Total FP COMP	4	>	1
Total FN	61	<	78
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	0.483
Average MCC ± 95% Confidence Intervals	0.543 ± 0.189
Sensitivity	0.558
Positive Predictive Value	0.440
Nr of predictions	7

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
3J3D_C	tRNA links to Rfam database...	0.76	0.95	0.62	18	939	11	9	2	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.18	0.21	0.18	7	1949	34	2	31	1	26
4AOB_A	SAM links to Rfam database...	0.39	0.41	0.39	12	1406	20	4	15	1	17
4ATO_G	-	0.72	1.00	0.54	7	207	6	6	0	0	0
4ENC_A	crcB links to Rfam database...	0.66	0.73	0.61	11	478	9	2	5	2	4
4JRC_A	-	0.56	0.65	0.50	11	600	11	3	8	0	6

Total Scores
MCC	0.470
Average MCC ± 95% Confidence Intervals	0.515 ± 0.306
Sensitivity	0.435
Positive Predictive Value	0.531
Nr of predictions	7

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
3J3D_C	tRNA links to Rfam database...	0.76	0.79	0.75	15	948	5	3	2	0	4
3W3S_B	tRNA-Sec links to Rfam database...	0.29	0.27	0.33	9	1962	18	2	16	0	24
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ATO_G	-	0.75	0.57	1.00	4	216	0	0	0	0	3
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9
4JRC_A	-	0.94	0.88	1.00	15	607	0	0	0	0	2

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