CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		Vsfold4
MCC	0.573	>	0.415
Average MCC ± 95% Confidence Intervals	0.523 ± 0.309	>	0.395 ± 0.291
Sensitivity	0.450	>	0.339
Positive Predictive Value	0.736	>	0.519
Total TP	109	>	82
Total TN	26996	>	26986
Total FP	41	<	90
Total FP CONTRA	7	>	4
Total FP INCONS	32	<	72
Total FP COMP	2	<	14
Total FN	133	<	160
P-value	0.0

Comparison of performance of Multilign(seed) and Vsfold4. 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 Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(seed) and Vsfold4. 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 Vsfold4).

Total Scores
MCC	0.573
Average MCC ± 95% Confidence Intervals	0.523 ± 0.309
Sensitivity	0.450
Positive Predictive Value	0.736
Nr of predictions	7

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
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

Total Scores
MCC	0.415
Average MCC ± 95% Confidence Intervals	0.395 ± 0.291
Sensitivity	0.339
Positive Predictive Value	0.519
Nr of predictions	7

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...	0.07	0.06	0.09	2	7481	32	2	18	12	31
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...	0.19	0.17	0.24	7	3887	22	1	21	0	35
3W3S_B	tRNA-Sec links to Rfam database...	0.67	0.58	0.79	23	4724	7	0	6	1	17
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4JF2_A	preQ1-II links to Rfam database...	0.66	0.52	0.84	16	2831	3	0	3	0	15

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