CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RSpredict(seed)
MCC	0.759	>	0.009
Average MCC ± 95% Confidence Intervals	0.781 ± 0.128	>	0.006 ± 0.018
Sensitivity	0.752	>	0.009
Positive Predictive Value	0.767	>	0.011
Total TP	477	>	6
Total TN	360763	<	360848
Total FP	227	<	557
Total FP CONTRA	30	<	106
Total FP INCONS	115	<	425
Total FP COMP	82	>	26
Total FN	157	<	628
P-value	0.0

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

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

Total Scores
MCC	0.009
Average MCC ± 95% Confidence Intervals	0.006 ± 0.018
Sensitivity	0.009
Positive Predictive Value	0.011
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...	0.00	0.00	0.00	0	56534	83	16	66	1	87
RFA_00628	rne5 links to Rfam database...	0.00	0.00	0.00	0	57206	85	25	60	0	86
RFA_00630	rne5 links to Rfam database...	0.07	0.07	0.07	6	56872	79	18	57	4	81
RFA_00816	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	23193	37	5	22	10	41
RFA_00817	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	21919	34	5	21	8	41
RFA_00818	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	20276	28	2	23	3	41
SRP_00241	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	45983	73	13	60	0	82
SRP_00331	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	37606	69	9	60	0	87
SRP_00340	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	41259	69	13	56	0	82

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