CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RDfolder
MCC	0.645	>	0.431
Average MCC ± 95% Confidence Intervals	0.612 ± 0.351	>	0.440 ± 0.379
Sensitivity	0.525	>	0.333
Positive Predictive Value	0.800	>	0.569
Total TP	104	>	66
Total TN	17651	<	17665
Total FP	28	<	51
Total FP CONTRA	2	<	4
Total FP INCONS	24	<	46
Total FP COMP	2	>	1
Total FN	94	<	132
P-value	0.0

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

Total Scores
MCC	0.645
Average MCC ± 95% Confidence Intervals	0.612 ± 0.351
Sensitivity	0.525
Positive Predictive Value	0.800
Nr of predictions	6

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

Total Scores
MCC	0.431
Average MCC ± 95% Confidence Intervals	0.440 ± 0.379
Sensitivity	0.333
Positive Predictive Value	0.569
Nr of predictions	6

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	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1526	14	2	12	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...	0.30	0.17	0.54	7	3903	6	0	6	0	35
3W3S_B	tRNA-Sec links to Rfam database...	0.27	0.23	0.33	9	4726	18	1	17	0	31
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31

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