CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		Vsfold5
MCC	0.628	>	0.447
Average MCC ± 95% Confidence Intervals	0.567 ± 0.311	>	0.406 ± 0.345
Sensitivity	0.575	>	0.450
Positive Predictive Value	0.697	>	0.462
Total TP	115	>	90
Total TN	11860	>	11830
Total FP	52	<	116
Total FP CONTRA	17	<	27
Total FP INCONS	33	<	78
Total FP COMP	2	<	11
Total FN	85	<	110
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	0.628
Average MCC ± 95% Confidence Intervals	0.567 ± 0.311
Sensitivity	0.575
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...	-0.03	0.00	0.00	0	516	12	2	10	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.19	0.20	0.19	3	2726	13	8	5	0	12
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
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

Total Scores
MCC	0.447
Average MCC ± 95% Confidence Intervals	0.406 ± 0.345
Sensitivity	0.450
Positive Predictive Value	0.462
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...	-0.03	0.00	0.00	0	515	13	0	13	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.08	2	2718	31	10	12	9	13
3RKF_A	Purine links to Rfam database...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25
3W3S_B	tRNA-Sec links to Rfam database...	0.83	0.85	0.82	28	1955	7	2	4	1	5
4AOB_A	SAM links to Rfam database...	0.21	0.21	0.25	6	1413	19	2	16	1	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.15	0.14	0.17	4	1825	19	3	16	0	24
4JF2_A	preQ1-II links to Rfam database...	0.96	1.00	0.92	24	1056	2	2	0	0	0

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