CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		Vsfold5
MCC	0.534	>	0.380
Average MCC ± 95% Confidence Intervals	0.487 ± 0.272	>	0.355 ± 0.302
Sensitivity	0.414	>	0.324
Positive Predictive Value	0.697	>	0.457
Total TP	115	>	90
Total TN	32130	>	32098
Total FP	52	<	116
Total FP CONTRA	8	<	10
Total FP INCONS	42	<	97
Total FP COMP	2	<	9
Total FN	163	<	188
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	0.534
Average MCC ± 95% Confidence Intervals	0.487 ± 0.272
Sensitivity	0.414
Positive Predictive Value	0.697
Nr of predictions	8

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...	-0.01	0.00	0.00	0	1528	12	1	11	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.13	0.09	0.19	3	7487	13	5	8	0	30
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
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

Total Scores
MCC	0.380
Average MCC ± 95% Confidence Intervals	0.355 ± 0.302
Sensitivity	0.324
Positive Predictive Value	0.457
Nr of predictions	8

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...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.06	0.06	0.08	2	7477	31	5	19	7	31
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
4JF2_A	preQ1-II links to Rfam database...	0.84	0.77	0.92	24	2824	2	1	1	0	7

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