CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		Contrafold
MCC	0.734	>	0.619
Average MCC ± 95% Confidence Intervals	0.740 ± 0.146	>	0.589 ± 0.178
Sensitivity	0.733	>	0.643
Positive Predictive Value	0.737	>	0.596
Total TP	493	>	433
Total TN	383507	>	383450
Total FP	263	<	388
Total FP CONTRA	42	<	83
Total FP INCONS	134	<	210
Total FP COMP	87	<	95
Total FN	180	<	240
P-value	1.60917593777e-09

Comparison of performance of Multilign(seed) and Contrafold. 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 Multilign(seed) and Contrafold).
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 Multilign(seed) and Contrafold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(seed) and Contrafold. 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 Multilign(seed) and Contrafold).

Total Scores
MCC	0.734
Average MCC ± 95% Confidence Intervals	0.740 ± 0.146
Sensitivity	0.733
Positive Predictive Value	0.737
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00619	-	0.37	0.41	0.34	16	22744	36	12	19	5	23
RFA_00626	rne5 links to Rfam database...	0.90	0.85	0.95	74	56538	20	0	4	16	13
RFA_00628	rne5 links to Rfam database...	0.92	0.88	0.95	76	57211	18	0	4	14	10
RFA_00630	rne5 links to Rfam database...	0.83	0.80	0.86	70	56872	29	0	11	18	17
RFA_00816	R2_retro_el links to Rfam database...	1.00	1.00	1.00	41	23179	12	0	0	12	0
RFA_00817	R2_retro_el links to Rfam database...	0.77	0.78	0.76	32	21903	13	5	5	3	9
RFA_00818	R2_retro_el links to Rfam database...	0.85	0.80	0.89	33	20264	12	1	3	8	8
SRP_00241	Plant_SRP links to Rfam database...	0.48	0.50	0.46	41	45967	50	15	33	2	41
SRP_00331	Metazoa_SRP links to Rfam database...	0.69	0.69	0.70	60	37589	29	2	24	3	27
SRP_00340	Metazoa_SRP links to Rfam database...	0.59	0.61	0.57	50	41240	44	7	31	6	32

Total Scores
MCC	0.619
Average MCC ± 95% Confidence Intervals	0.589 ± 0.178
Sensitivity	0.643
Positive Predictive Value	0.596
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00619	-	0.36	0.41	0.33	16	22742	45	10	23	12	23
RFA_00626	rne5 links to Rfam database...	0.91	0.87	0.94	76	56535	26	1	4	21	11
RFA_00628	rne5 links to Rfam database...	0.91	0.88	0.94	76	57210	25	0	5	20	10
RFA_00630	rne5 links to Rfam database...	0.77	0.77	0.77	67	56866	34	6	14	14	20
RFA_00816	R2_retro_el links to Rfam database...	0.72	0.73	0.71	30	23178	20	8	4	8	11
RFA_00817	R2_retro_el links to Rfam database...	0.11	0.12	0.10	5	21893	47	12	35	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.57	0.61	0.53	25	20254	32	11	11	10	16
SRP_00241	Plant_SRP links to Rfam database...	0.51	0.55	0.47	45	45961	53	14	36	3	37
SRP_00331	Metazoa_SRP links to Rfam database...	0.52	0.54	0.50	47	37581	50	10	37	3	40
SRP_00340	Metazoa_SRP links to Rfam database...	0.51	0.56	0.47	46	41230	56	11	41	4	36

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