CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Cylofold		RNASampler(seed)
MCC	0.775	>	0.678
Average MCC ± 95% Confidence Intervals	0.791 ± 0.195	>	0.644 ± 0.295
Sensitivity	0.766	>	0.570
Positive Predictive Value	0.791	<	0.818
Total TP	121	>	90
Total TN	9449	<	9492
Total FP	43	>	26
Total FP CONTRA	12	>	5
Total FP INCONS	20	>	15
Total FP COMP	11	>	6
Total FN	37	<	68
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	0.775
Average MCC ± 95% Confidence Intervals	0.791 ± 0.195
Sensitivity	0.766
Positive Predictive Value	0.791
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_A	Gammaretro_CES links to Rfam database...	0.93	0.87	1.00	20	743	0	0	0	0	3
2L1F_B	Gammaretro_CES links to Rfam database...	0.93	0.88	1.00	21	770	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

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.644 ± 0.295
Sensitivity	0.570
Positive Predictive Value	0.818
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_A	Gammaretro_CES links to Rfam database...	0.83	0.70	1.00	16	747	0	0	0	0	7
2L1F_B	Gammaretro_CES links to Rfam database...	0.84	0.71	1.00	17	774	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

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