CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		Multilign(seed)
MCC	0.619	>	0.575
Average MCC ± 95% Confidence Intervals	0.618 ± 0.055	>	0.578 ± 0.076
Sensitivity	0.536	=	0.536
Positive Predictive Value	0.721	>	0.625
Total TP	75	=	75
Total TN	15714	>	15698
Total FP	29	<	45
Total FP CONTRA	19	>	5
Total FP INCONS	10	<	40
Total FP COMP	0	=	0
Total FN	65	=	65
P-value	0.0

Comparison of performance of PETfold_pre2.0(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 PETfold_pre2.0(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 PETfold_pre2.0(seed) and Multilign(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(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 PETfold_pre2.0(seed) and Multilign(seed)).

Total Scores
MCC	0.619
Average MCC ± 95% Confidence Intervals	0.618 ± 0.055
Sensitivity	0.536
Positive Predictive Value	0.721
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	3	1	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	3	1	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	2002	4	3	1	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00808	RydC links to Rfam database...	0.71	0.56	0.90	9	2006	1	1	0	0	7
RFA_00809	RydC links to Rfam database...	0.47	0.38	0.60	6	2135	4	0	4	0	10

Total Scores
MCC	0.575
Average MCC ± 95% Confidence Intervals	0.578 ± 0.076
Sensitivity	0.536
Positive Predictive Value	0.625
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	0	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1876	5	0	5	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	2	0	2	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1938	5	0	5	0	8
RFA_00808	RydC links to Rfam database...	0.60	0.56	0.64	9	2002	5	0	5	0	7
RFA_00809	RydC links to Rfam database...	0.37	0.38	0.38	6	2129	10	1	9	0	10

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