CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		RSpredict(20)
MCC	0.558	>	0.419
Average MCC ± 95% Confidence Intervals	0.569 ± 0.212	>	0.428 ± 0.198
Sensitivity	0.544	>	0.388
Positive Predictive Value	0.580	>	0.462
Total TP	112	>	80
Total TN	22994	<	23014
Total FP	129	>	117
Total FP CONTRA	37	>	35
Total FP INCONS	44	<	58
Total FP COMP	48	>	24
Total FN	94	<	126
P-value	8.70625200892e-09

Comparison of performance of ContextFold and RSpredict(20). 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 ContextFold and RSpredict(20)).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for ContextFold and RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and RSpredict(20). 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 ContextFold and RSpredict(20)).

Total Scores
MCC	0.558
Average MCC ± 95% Confidence Intervals	0.569 ± 0.212
Sensitivity	0.544
Positive Predictive Value	0.580
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J3D_C	tRNA links to Rfam database...	0.79	0.79	0.79	15	949	4	3	1	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2722	29	12	8	9	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.42	0.31	8	4735	32	9	9	14	11
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.41	0.48	12	5349	23	4	9	10	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.77	0.71	0.85	17	1182	3	2	1	0	7

Total Scores
MCC	0.419
Average MCC ± 95% Confidence Intervals	0.428 ± 0.198
Sensitivity	0.388
Positive Predictive Value	0.462
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J3D_C	tRNA links to Rfam database...	0.82	0.84	0.80	16	948	4	3	1	0	3
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	19	5	13	1	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.47	0.38	9	4737	26	9	6	11	10
3ZEX_C	5_8S_rRNA links to Rfam database...	0.34	0.31	0.38	9	5350	19	3	12	4	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.30	0.21	6	4487	30	12	11	7	14
4AOB_A	SAM links to Rfam database...	0.33	0.21	0.55	6	1426	5	1	4	0	23
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.51	0.40	0.67	6	487	3	0	3	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.13	0.33	3	1193	6	1	5	0	21

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