CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAfold		CMfinder(seed)
MCC	0.466	>	0.350
Average MCC ± 95% Confidence Intervals	0.447 ± 0.103	>	0.358 ± 0.060
Sensitivity	0.468	>	0.159
Positive Predictive Value	0.465	<	0.770
Total TP	688	>	234
Total TN	1035170	<	1036346
Total FP	961	>	77
Total FP CONTRA	174	>	3
Total FP INCONS	618	>	67
Total FP COMP	169	>	7
Total FN	782	<	1236
P-value	2.94377603181e-08

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

Total Scores
MCC	0.466
Average MCC ± 95% Confidence Intervals	0.447 ± 0.103
Sensitivity	0.468
Positive Predictive Value	0.465
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...	0.21	0.22	0.21	25	103623	116	12	80	24	90
CRW_00016	Intron_gpI links to Rfam database...	0.64	0.62	0.67	74	77311	47	5	31	11	46
CRW_00610	Intron_gpI links to Rfam database...	0.21	0.21	0.22	17	36239	59	7	52	0	64
CRW_00613	Intron_gpI links to Rfam database...	0.65	0.60	0.70	47	34913	28	1	19	8	31
CRW_00614	Intron_gpI links to Rfam database...	0.16	0.19	0.14	11	121692	131	25	43	63	46
CRW_00618	Intron_gpI links to Rfam database...	0.12	0.13	0.12	8	56212	82	13	47	22	53
CRW_00633	Intron_gpI links to Rfam database...	0.44	0.43	0.45	46	63444	58	13	43	2	60
CRW_00634	Intron_gpI links to Rfam database...	0.50	0.52	0.49	49	64519	57	10	42	5	45
CRW_00670	Intron_gpI links to Rfam database...	0.69	0.68	0.71	82	70009	36	9	25	2	38
CRW_00671	Intron_gpI links to Rfam database...	0.60	0.59	0.61	69	62722	49	6	38	5	48
CRW_00672	Intron_gpI links to Rfam database...	0.48	0.50	0.47	55	72273	65	19	43	3	56
CRW_00674	Intron_gpI links to Rfam database...	0.53	0.53	0.52	66	83310	62	12	48	2	58
CRW_00676	Intron_gpI links to Rfam database...	0.54	0.56	0.52	64	93406	74	17	41	16	51
CRW_00692	Intron_gpI links to Rfam database...	0.40	0.42	0.38	38	68536	66	24	37	5	52
PDB_00827	Intron_gpI links to Rfam database...	0.50	0.46	0.55	37	26961	31	1	29	1	44

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.