CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		Mastr(seed)
MCC	0.759	>	0.491
Average MCC ± 95% Confidence Intervals	0.781 ± 0.128	>	0.254 ± 0.298
Sensitivity	0.752	>	0.274
Positive Predictive Value	0.767	<	0.879
Total TP	477	>	174
Total TN	360763	<	361187
Total FP	227	>	47
Total FP CONTRA	30	>	2
Total FP INCONS	115	>	22
Total FP COMP	82	>	23
Total FN	157	<	460
P-value	0.0

Comparison of performance of Multilign(seed) and Mastr(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 Mastr(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 Mastr(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(seed) and Mastr(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 Mastr(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	0.491
Average MCC ± 95% Confidence Intervals	0.254 ± 0.298
Sensitivity	0.274
Positive Predictive Value	0.879
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...	0.61	0.51	0.75	44	56557	22	2	13	7	43
RFA_00628	rne5 links to Rfam database...	0.88	0.80	0.96	69	57219	11	0	3	8	17
RFA_00630	rne5 links to Rfam database...	0.80	0.70	0.91	61	56886	14	0	6	8	26
RFA_00816	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	23220	0	0	0	0	41
RFA_00817	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	21945	0	0	0	0	41
RFA_00818	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	20301	0	0	0	0	41
SRP_00241	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	82
SRP_00331	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	37675	0	0	0	0	87
SRP_00340	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	41328	0	0	0	0	82

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