CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		RNASampler(seed)
MCC	0.725	>	0.664
Average MCC ± 95% Confidence Intervals	0.752 ± 0.188	>	0.638 ± 0.247
Sensitivity	0.712	>	0.534
Positive Predictive Value	0.747	<	0.836
Total TP	136	>	102
Total TN	11409	<	11469
Total FP	58	>	27
Total FP CONTRA	13	>	5
Total FP INCONS	33	>	15
Total FP COMP	12	>	7
Total FN	55	<	89
P-value	0.0

Comparison of performance of Cylofold and RNASampler(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 Cylofold and RNASampler(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold and RNASampler(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 Cylofold and RNASampler(seed)).

Total Scores
MCC	0.725
Average MCC ± 95% Confidence Intervals	0.752 ± 0.188
Sensitivity	0.712
Positive Predictive Value	0.747
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_B	Gammaretro_CES links to Rfam database...	0.93	0.88	1.00	21	770	0	0	0	0	3
2L1F_A	Gammaretro_CES links to Rfam database...	0.93	0.87	1.00	20	743	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	30	9	11	10	11
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...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3W3S_B	tRNA-Sec links to Rfam database...	0.48	0.45	0.52	15	1960	15	1	13	1	18

Total Scores
MCC	0.664
Average MCC ± 95% Confidence Intervals	0.638 ± 0.247
Sensitivity	0.534
Positive Predictive Value	0.836
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_B	Gammaretro_CES links to Rfam database...	0.84	0.71	1.00	17	774	0	0	0	0	7
2L1F_A	Gammaretro_CES links to Rfam database...	0.83	0.70	1.00	16	747	0	0	0	0	7
2L94_A	HIV_FE links to Rfam database...	0.70	0.56	0.91	10	346	2	0	1	1	8
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	518	10	0	10	0	18
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.50	0.58	11	4745	13	5	3	5	11
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...	0.72	0.55	0.94	16	1516	1	0	1	0	13
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.36	1.00	12	1977	1	0	0	1	21

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