CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		Cylofold
MCC	0.667	>	0.662
Average MCC ± 95% Confidence Intervals	0.649 ± 0.286	<	0.695 ± 0.271
Sensitivity	0.601	<	0.614
Positive Predictive Value	0.754	>	0.729
Total TP	95	<	97
Total TN	7054	>	7047
Total FP	32	<	37
Total FP CONTRA	9	<	14
Total FP INCONS	22	=	22
Total FP COMP	1	=	1
Total FN	63	>	61
P-value	0.0

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

Total Scores
MCC	0.667
Average MCC ± 95% Confidence Intervals	0.649 ± 0.286
Sensitivity	0.601
Positive Predictive Value	0.754
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.79	0.71	0.87	20	1825	3	1	2	0	8

Total Scores
MCC	0.662
Average MCC ± 95% Confidence Intervals	0.695 ± 0.271
Sensitivity	0.614
Positive Predictive Value	0.729
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.23	0.18	0.31	5	1832	11	7	4	0	23

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