CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		Afold
MCC	0.647	>	0.632
Average MCC ± 95% Confidence Intervals	0.672 ± 0.155	>	0.613 ± 0.141
Sensitivity	0.649	=	0.649
Positive Predictive Value	0.655	>	0.627
Total TP	133	=	133
Total TN	13010	>	13001
Total FP	81	<	103
Total FP CONTRA	17	<	19
Total FP INCONS	53	<	60
Total FP COMP	11	<	24
Total FN	72	=	72
P-value	1.99684630116e-06

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

Total Scores
MCC	0.647
Average MCC ± 95% Confidence Intervals	0.672 ± 0.155
Sensitivity	0.649
Positive Predictive Value	0.655
Nr of predictions	10

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
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
3ADB_C	-	0.84	0.82	0.87	27	1788	4	0	4	0	6
3NKB_B	-	0.46	0.42	0.53	8	720	7	0	7	0	11
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	30	9	11	10	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.48	0.45	0.52	15	1960	15	1	13	1	18
4ATO_G	-	0.88	1.00	0.78	7	211	2	2	0	0	0
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0

Total Scores
MCC	0.632
Average MCC ± 95% Confidence Intervals	0.613 ± 0.141
Sensitivity	0.649
Positive Predictive Value	0.627
Nr of predictions	10

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	6	0	5	1	7
2M58_A	-	0.40	0.42	0.42	5	532	8	1	6	1	7
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.55	0.56	18	1957	15	4	10	1	15
4ATO_G	-	0.38	0.43	0.38	3	212	6	5	0	1	4
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

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