CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Alterna
MCC	0.743	>	0.584
Average MCC ± 95% Confidence Intervals	0.754 ± 0.236	>	0.597 ± 0.298
Sensitivity	0.592	>	0.495
Positive Predictive Value	0.938	>	0.699
Total TP	61	>	51
Total TN	9065	>	9057
Total FP	5	<	24
Total FP CONTRA	0	<	2
Total FP INCONS	4	<	20
Total FP COMP	1	<	2
Total FN	42	<	52
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	0.743
Average MCC ± 95% Confidence Intervals	0.754 ± 0.236
Sensitivity	0.592
Positive Predictive Value	0.938
Nr of predictions	3

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20

Total Scores
MCC	0.584
Average MCC ± 95% Confidence Intervals	0.597 ± 0.298
Sensitivity	0.495
Positive Predictive Value	0.699
Nr of predictions	3

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26

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