CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		Multilign(seed)
MCC	0.687	>	0.672
Average MCC ± 95% Confidence Intervals	0.672 ± 0.337	>	0.633 ± 0.349
Sensitivity	0.654	>	0.615
Positive Predictive Value	0.736	<	0.748
Total TP	117	>	110
Total TN	8399	<	8411
Total FP	45	>	39
Total FP CONTRA	12	>	9
Total FP INCONS	30	>	28
Total FP COMP	3	>	2
Total FN	62	<	69
P-value	0.0

Comparison of performance of CentroidHomfold-LAST and Multilign(seed). 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 CentroidHomfold‑LAST and Multilign(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST and Multilign(seed). 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 CentroidHomfold‑LAST and Multilign(seed)).

Total Scores
MCC	0.687
Average MCC ± 95% Confidence Intervals	0.672 ± 0.337
Sensitivity	0.654
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
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	517	11	0	11	0	18
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.77	0.66	0.90	19	1512	2	1	1	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.88	1.00	29	1960	1	0	0	1	4
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	1	0	0	1	8
4FRN_A	AdoCbl-variant links to Rfam database...	0.37	0.46	0.32	13	1807	28	11	17	0	15

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

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