CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		CRWrnafold
MCC	0.624	>	0.563
Average MCC ± 95% Confidence Intervals	0.627 ± 0.276	>	0.556 ± 0.288
Sensitivity	0.619	>	0.554
Positive Predictive Value	0.647	>	0.592
Total TP	86	>	77
Total TN	6020	<	6023
Total FP	49	<	59
Total FP CONTRA	13	<	19
Total FP INCONS	34	=	34
Total FP COMP	2	<	6
Total FN	53	<	62
P-value	0.0

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

Total Scores
MCC	0.624
Average MCC ± 95% Confidence Intervals	0.627 ± 0.276
Sensitivity	0.619
Positive Predictive Value	0.647
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
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
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	0.563
Average MCC ± 95% Confidence Intervals	0.556 ± 0.288
Sensitivity	0.554
Positive Predictive Value	0.592
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
3J0L_a	-	0.39	0.36	0.44	4	402	6	3	2	1	7
3SD1_A	THF links to Rfam database...	0.63	0.66	0.61	19	1502	12	6	6	0	10
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	8	4	3	1	9
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	2	0	0	2	4

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