CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(seed)		Multilign(seed)
MCC	0.794	>	0.759
Average MCC ± 95% Confidence Intervals	0.789 ± 0.124	>	0.781 ± 0.128
Sensitivity	0.696	<	0.752
Positive Predictive Value	0.907	>	0.767
Total TP	441	<	477
Total TN	360899	>	360763
Total FP	87	<	227
Total FP CONTRA	7	<	30
Total FP INCONS	38	<	115
Total FP COMP	42	<	82
Total FN	193	>	157
P-value	0.0

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

Total Scores
MCC	0.794
Average MCC ± 95% Confidence Intervals	0.789 ± 0.124
Sensitivity	0.696
Positive Predictive Value	0.907
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00626	rne5 links to Rfam database...	0.97	0.94	1.00	82	56534	6	0	0	6	5
RFA_00628	rne5 links to Rfam database...	0.97	0.94	1.00	81	57210	6	0	0	6	5
RFA_00630	rne5 links to Rfam database...	0.92	0.87	0.96	76	56874	12	0	3	9	11
RFA_00816	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	23192	0	0	0	0	13
RFA_00817	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	21917	0	0	0	0	13
RFA_00818	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	20273	0	0	0	0	13
SRP_00241	Plant_SRP links to Rfam database...	0.59	0.48	0.72	39	46002	22	4	11	7	43
SRP_00331	Metazoa_SRP links to Rfam database...	0.58	0.47	0.72	41	37618	21	1	15	5	46
SRP_00340	Metazoa_SRP links to Rfam database...	0.60	0.46	0.78	38	41279	20	2	9	9	44

Total Scores
MCC	0.759
Average MCC ± 95% Confidence Intervals	0.781 ± 0.128
Sensitivity	0.752
Positive Predictive Value	0.767
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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

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