CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Afold
MCC	0.598	>	0.577
Average MCC ± 95% Confidence Intervals	0.588 ± 0.746	<	0.639 ± 0.972
Sensitivity	0.525	<	0.610
Positive Predictive Value	0.689	>	0.554
Total TP	31	<	36
Total TN	5809	>	5789
Total FP	18	<	46
Total FP CONTRA	1	<	11
Total FP INCONS	13	<	18
Total FP COMP	4	<	17
Total FN	28	>	23
P-value	0.0

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

Total Scores
MCC	0.598
Average MCC ± 95% Confidence Intervals	0.588 ± 0.746
Sensitivity	0.525
Positive Predictive Value	0.689
Nr of predictions	3

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
4A1C_2	5_8S_rRNA links to Rfam database...	0.27	0.25	0.29	5	4499	16	1	11	4	15
4ENB_A	crcB links to Rfam database...	0.63	0.47	0.88	7	464	1	0	1	0	8

Total Scores
MCC	0.577
Average MCC ± 95% Confidence Intervals	0.639 ± 0.972
Sensitivity	0.610
Positive Predictive Value	0.554
Nr of predictions	3

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

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