CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Cylofold
MCC	0.826	>	0.780
Average MCC ± 95% Confidence Intervals	0.802 ± 0.111	<	0.811 ± 0.191
Sensitivity	0.752	=	0.752
Positive Predictive Value	0.915	>	0.819
Total TP	118	=	118
Total TN	7096	>	7081
Total FP	13	<	28
Total FP CONTRA	3	<	9
Total FP INCONS	8	<	17
Total FP COMP	2	=	2
Total FN	39	=	39
P-value	0.0

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

Total Scores
MCC	0.826
Average MCC ± 95% Confidence Intervals	0.802 ± 0.111
Sensitivity	0.752
Positive Predictive Value	0.915
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	1	1	0	0	1
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
4AOB_A	SAM links to Rfam database...	0.87	0.83	0.92	24	1411	4	0	2	2	5
4ENB_A	crcB links to Rfam database...	0.63	0.47	0.88	7	464	1	0	1	0	8
4ENC_A	crcB links to Rfam database...	0.64	0.53	0.80	8	486	2	0	2	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.75	0.95	18	1183	1	0	1	0	6

Total Scores
MCC	0.780
Average MCC ± 95% Confidence Intervals	0.811 ± 0.191
Sensitivity	0.752
Positive Predictive Value	0.819
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3

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