CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		Cylofold
MCC	0.672	>	0.605
Average MCC ± 95% Confidence Intervals	0.633 ± 0.349	>	0.625 ± 0.254
Sensitivity	0.615	>	0.559
Positive Predictive Value	0.748	>	0.671
Total TP	110	>	100
Total TN	8411	>	8409
Total FP	39	<	52
Total FP CONTRA	9	<	14
Total FP INCONS	28	<	35
Total FP COMP	2	<	3
Total FN	69	<	79
P-value	0.0

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

Total Scores
MCC	0.672
Average MCC ± 95% Confidence Intervals	0.633 ± 0.349
Sensitivity	0.615
Positive Predictive Value	0.748
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...	0.97	0.94	1.00	17	340	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	516	12	2	10	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...	0.66	0.66	0.68	19	1505	9	4	5	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.92	0.88	0.97	29	1959	2	0	1	1	4
4AOB_A	SAM links to Rfam database...	0.73	0.66	0.83	19	1414	5	1	3	1	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.27	0.21	0.35	6	1831	11	2	9	0	22

Total Scores
MCC	0.605
Average MCC ± 95% Confidence Intervals	0.625 ± 0.254
Sensitivity	0.559
Positive Predictive Value	0.671
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
3W3S_B	tRNA-Sec links to Rfam database...	0.48	0.45	0.52	15	1960	15	1	13	1	18
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
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.