CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(20)		Afold
MCC	0.835	>	0.569
Average MCC ± 95% Confidence Intervals	0.836 ± 0.170	>	0.564 ± 1.229
Sensitivity	0.737	>	0.500
Positive Predictive Value	0.949	>	0.655
Total TP	56	>	38
Total TN	8025	<	8026
Total FP	3	<	21
Total FP CONTRA	1	<	5
Total FP INCONS	2	<	15
Total FP COMP	0	<	1
Total FN	20	<	38
P-value	0.0

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

Total Scores
MCC	0.835
Average MCC ± 95% Confidence Intervals	0.836 ± 0.170
Sensitivity	0.737
Positive Predictive Value	0.949
Nr of predictions	3

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00571	tRNA links to Rfam database...	0.76	0.68	0.85	17	3301	3	1	2	0	8
PDB_00828	Purine links to Rfam database...	0.86	0.74	1.00	20	2465	0	0	0	0	7
PDB_00829	Purine links to Rfam database...	0.89	0.79	1.00	19	2259	0	0	0	0	5

Total Scores
MCC	0.569
Average MCC ± 95% Confidence Intervals	0.564 ± 1.229
Sensitivity	0.500
Positive Predictive Value	0.655
Nr of predictions	3

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00571	tRNA links to Rfam database...	-0.01	0.00	0.00	0	3302	20	5	14	1	25
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.82	0.71	0.94	17	2260	1	0	1	0	7

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