CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		CMfinder(seed)
MCC	0.632	>	0.350
Average MCC ± 95% Confidence Intervals	0.610 ± 0.124	>	0.358 ± 0.060
Sensitivity	0.573	>	0.159
Positive Predictive Value	0.698	<	0.770
Total TP	843	>	234
Total TN	1035443	<	1036346
Total FP	465	>	77
Total FP CONTRA	98	>	3
Total FP INCONS	266	>	67
Total FP COMP	101	>	7
Total FN	627	<	1236
P-value	1.96907987703e-08

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

Total Scores
MCC	0.632
Average MCC ± 95% Confidence Intervals	0.610 ± 0.124
Sensitivity	0.573
Positive Predictive Value	0.698
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...	0.33	0.26	0.42	30	103669	55	7	34	14	85
CRW_00016	Intron_gpI links to Rfam database...	0.75	0.67	0.83	80	77325	26	6	10	10	40
CRW_00610	Intron_gpI links to Rfam database...	0.61	0.54	0.68	44	36250	21	6	15	0	37
CRW_00613	Intron_gpI links to Rfam database...	0.86	0.78	0.94	61	34915	13	1	3	9	17
CRW_00614	Intron_gpI links to Rfam database...	0.13	0.14	0.13	8	121707	95	15	41	39	49
CRW_00618	Intron_gpI links to Rfam database...	0.25	0.25	0.26	15	56223	56	5	37	14	46
CRW_00633	Intron_gpI links to Rfam database...	0.64	0.58	0.72	61	63461	25	5	19	1	45
CRW_00634	Intron_gpI links to Rfam database...	0.60	0.56	0.65	53	64538	30	10	19	1	41
CRW_00670	Intron_gpI links to Rfam database...	0.83	0.78	0.87	94	70017	14	6	8	0	26
CRW_00671	Intron_gpI links to Rfam database...	0.82	0.74	0.92	86	62742	8	1	6	1	31
CRW_00672	Intron_gpI links to Rfam database...	0.76	0.72	0.80	80	72290	24	8	12	4	31
CRW_00674	Intron_gpI links to Rfam database...	0.75	0.69	0.83	85	83333	20	7	11	2	39
CRW_00676	Intron_gpI links to Rfam database...	0.47	0.44	0.51	51	93428	52	14	35	3	64
CRW_00692	Intron_gpI links to Rfam database...	0.56	0.47	0.68	42	68573	21	7	13	1	48
PDB_00827	Intron_gpI links to Rfam database...	0.79	0.65	0.95	53	26972	5	0	3	2	28

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.