CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Alterna
MCC	0.836	>	0.673
Average MCC ± 95% Confidence Intervals	0.839 ± 0.318	>	0.688 ± 1.709
Sensitivity	0.774	>	0.660
Positive Predictive Value	0.911	>	0.700
Total TP	41	>	35
Total TN	2354	>	2349
Total FP	4	<	15
Total FP CONTRA	2	<	5
Total FP INCONS	2	<	10
Total FP COMP	0	=	0
Total FN	12	<	18
P-value	0.0

Comparison of performance of PPfold(20) and Alterna. 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 PPfold(20) and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and Alterna. 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 PPfold(20) and Alterna).

Total Scores
MCC	0.836
Average MCC ± 95% Confidence Intervals	0.839 ± 0.318
Sensitivity	0.774
Positive Predictive Value	0.911
Nr of predictions	2

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3RKF_A	Purine links to Rfam database...	0.86	0.79	0.95	19	846	1	0	1	0	5
3SD1_A	THF links to Rfam database...	0.81	0.76	0.88	22	1508	3	2	1	0	7

Total Scores
MCC	0.673
Average MCC ± 95% Confidence Intervals	0.688 ± 1.709
Sensitivity	0.660
Positive Predictive Value	0.700
Nr of predictions	2

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3RKF_A	Purine links to Rfam database...	0.82	0.79	0.86	19	844	3	1	2	0	5
3SD1_A	THF links to Rfam database...	0.55	0.55	0.57	16	1505	12	4	8	0	13

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