CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Cylofold		Carnac(20)
MCC	0.731	>	0.659
Average MCC ± 95% Confidence Intervals	0.754 ± 0.230	>	0.510 ± 0.337
Sensitivity	0.712	>	0.473
Positive Predictive Value	0.757	<	0.926
Total TP	131	>	87
Total TN	14235	<	14314
Total FP	55	>	11
Total FP CONTRA	16	>	3
Total FP INCONS	26	>	4
Total FP COMP	13	>	4
Total FN	53	<	97
P-value	0.0

Comparison of performance of Cylofold and Carnac(20). 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 Carnac(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold and Carnac(20). 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 Carnac(20)).

Total Scores
MCC	0.731
Average MCC ± 95% Confidence Intervals	0.754 ± 0.230
Sensitivity	0.712
Positive Predictive Value	0.757
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	30	9	11	10	11
3PDR_A	ykoK links to Rfam database...	0.86	0.78	0.95	39	4799	4	1	1	2	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
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

Total Scores
MCC	0.659
Average MCC ± 95% Confidence Intervals	0.510 ± 0.337
Sensitivity	0.473
Positive Predictive Value	0.926
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3O58_3	5_8S_rRNA links to Rfam database...	0.60	0.36	1.00	8	4756	1	0	0	1	14
3PDR_A	ykoK links to Rfam database...	0.75	0.58	0.97	29	4810	3	1	0	2	21
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
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	14	1418	6	2	3	1	15
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15

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