CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ProbKnot		CMfinder(seed)
MCC	0.554	>	0.350
Average MCC ± 95% Confidence Intervals	0.538 ± 0.119	>	0.358 ± 0.060
Sensitivity	0.550	>	0.159
Positive Predictive Value	0.560	<	0.770
Total TP	809	>	234
Total TN	1035205	<	1036346
Total FP	833	>	77
Total FP CONTRA	136	>	3
Total FP INCONS	500	>	67
Total FP COMP	197	>	7
Total FN	661	<	1236
P-value	2.12160100812e-08

Comparison of performance of ProbKnot and CMfinder(seed). 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 ProbKnot and CMfinder(seed)).
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 ProbKnot and CMfinder(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot and CMfinder(seed). 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 ProbKnot and CMfinder(seed)).

Total Scores
MCC	0.554
Average MCC ± 95% Confidence Intervals	0.538 ± 0.119
Sensitivity	0.550
Positive Predictive Value	0.560
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00013	Intron_gpI links to Rfam database...	0.39	0.37	0.42	43	103637	84	9	51	24	72
CRW_00016	Intron_gpI links to Rfam database...	0.48	0.45	0.50	54	77314	68	6	47	15	66
CRW_00610	Intron_gpI links to Rfam database...	0.44	0.44	0.43	36	36232	49	8	39	2	45
CRW_00613	Intron_gpI links to Rfam database...	0.84	0.82	0.86	64	34906	18	0	10	8	14
CRW_00614	Intron_gpI links to Rfam database...	0.14	0.16	0.12	9	121698	120	17	47	56	48
CRW_00618	Intron_gpI links to Rfam database...	0.18	0.20	0.16	12	56207	83	15	46	22	49
CRW_00633	Intron_gpI links to Rfam database...	0.62	0.59	0.65	63	63449	38	9	25	4	43
CRW_00634	Intron_gpI links to Rfam database...	0.50	0.49	0.52	46	64531	48	10	33	5	48
CRW_00670	Intron_gpI links to Rfam database...	0.57	0.58	0.56	70	70001	57	11	43	3	50
CRW_00671	Intron_gpI links to Rfam database...	0.79	0.77	0.80	90	62723	28	6	16	6	27
CRW_00672	Intron_gpI links to Rfam database...	0.76	0.78	0.74	87	72272	41	10	21	10	24
CRW_00674	Intron_gpI links to Rfam database...	0.68	0.67	0.70	83	83317	41	8	28	5	41
CRW_00676	Intron_gpI links to Rfam database...	0.59	0.58	0.60	67	93416	63	8	37	18	48
CRW_00692	Intron_gpI links to Rfam database...	0.33	0.34	0.32	31	68537	84	18	49	17	59
PDB_00827	Intron_gpI links to Rfam database...	0.76	0.67	0.86	54	26965	11	1	8	2	27

Total Scores
MCC	0.350
Average MCC ± 95% Confidence Intervals	0.358 ± 0.060
Sensitivity	0.159
Positive Predictive Value	0.770
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00013	Intron_gpI links to Rfam database...	0.37	0.14	1.00	16	103724	0	0	0	0	99
CRW_00016	Intron_gpI links to Rfam database...	0.36	0.14	0.89	17	77402	2	0	2	0	103
CRW_00610	Intron_gpI links to Rfam database...	0.49	0.31	0.78	25	36283	7	1	6	0	56
CRW_00613	Intron_gpI links to Rfam database...	0.54	0.33	0.87	26	34950	4	0	4	0	52
CRW_00614	Intron_gpI links to Rfam database...	0.46	0.25	0.88	14	121755	9	0	2	7	43
CRW_00618	Intron_gpI links to Rfam database...	0.36	0.13	1.00	8	56272	0	0	0	0	53
CRW_00633	Intron_gpI links to Rfam database...	0.32	0.12	0.81	13	63530	3	1	2	0	93
CRW_00634	Intron_gpI links to Rfam database...	0.40	0.17	0.94	16	64603	1	0	1	0	78
CRW_00670	Intron_gpI links to Rfam database...	0.32	0.18	0.55	22	70085	18	0	18	0	98
CRW_00671	Intron_gpI links to Rfam database...	0.20	0.09	0.41	11	62808	16	0	16	0	106
CRW_00672	Intron_gpI links to Rfam database...	0.38	0.15	0.94	17	72372	1	0	1	0	94
CRW_00674	Intron_gpI links to Rfam database...	0.40	0.17	0.95	21	83414	1	0	1	0	103
CRW_00676	Intron_gpI links to Rfam database...	0.12	0.04	0.33	5	93513	10	1	9	0	110
CRW_00692	Intron_gpI links to Rfam database...	0.41	0.17	1.00	15	68620	0	0	0	0	75
PDB_00827	Intron_gpI links to Rfam database...	0.25	0.10	0.62	8	27015	5	0	5	0	73

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