CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		Vsfold5
MCC	0.590	>	0.415
Average MCC ± 95% Confidence Intervals	0.558 ± 0.311	>	0.411 ± 0.362
Sensitivity	0.470	>	0.350
Positive Predictive Value	0.748	>	0.503
Total TP	110	>	82
Total TN	22785	>	22769
Total FP	39	<	83
Total FP CONTRA	3	<	4
Total FP INCONS	34	<	77
Total FP COMP	2	=	2
Total FN	124	<	152
P-value	0.0

Comparison of performance of Multilign(seed) and Vsfold5. 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 Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(seed) and Vsfold5. 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 Vsfold5).

Total Scores
MCC	0.590
Average MCC ± 95% Confidence Intervals	0.558 ± 0.311
Sensitivity	0.470
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...	0.92	0.85	1.00	17	973	0	0	0	0	3
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	1	11	0	20
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.55	0.45	0.68	19	3888	9	1	8	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.84	0.73	0.97	29	4723	2	0	1	1	11
4AOB_A	SAM links to Rfam database...	0.61	0.45	0.83	19	4348	5	0	4	1	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.24	0.17	0.35	6	5134	11	1	10	0	30

Total Scores
MCC	0.415
Average MCC ± 95% Confidence Intervals	0.411 ± 0.362
Sensitivity	0.350
Positive Predictive Value	0.503
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...	0.95	0.90	1.00	18	972	0	0	0	0	2
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
3RKF_A	Purine links to Rfam database...	0.75	0.65	0.88	22	2186	3	0	3	0	12
3SD1_A	THF links to Rfam database...	0.11	0.10	0.15	4	3890	22	0	22	0	38
3W3S_B	tRNA-Sec links to Rfam database...	0.76	0.70	0.82	28	4719	7	1	5	1	12
4AOB_A	SAM links to Rfam database...	0.18	0.14	0.25	6	4347	19	1	17	1	36
4FRN_A	AdoCbl-variant links to Rfam database...	0.13	0.11	0.17	4	5128	19	2	17	0	32

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