CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		TurboFold(seed)
MCC	0.773	>	0.680
Average MCC ± 95% Confidence Intervals	0.806 ± 0.208	>	0.671 ± 0.302
Sensitivity	0.743	>	0.622
Positive Predictive Value	0.815	>	0.760
Total TP	110	>	92
Total TN	5554	<	5568
Total FP	27	<	31
Total FP CONTRA	7	<	8
Total FP INCONS	18	<	21
Total FP COMP	2	=	2
Total FN	38	<	56
P-value	0.0

Comparison of performance of Cylofold and TurboFold(seed). 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 Cylofold and TurboFold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold and TurboFold(seed). 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 Cylofold and TurboFold(seed)).

Total Scores
MCC	0.773
Average MCC ± 95% Confidence Intervals	0.806 ± 0.208
Sensitivity	0.743
Positive Predictive Value	0.815
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
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

Total Scores
MCC	0.680
Average MCC ± 95% Confidence Intervals	0.671 ± 0.302
Sensitivity	0.622
Positive Predictive Value	0.760
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
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...	0.67	0.59	0.77	17	1415	6	2	3	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

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