CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Cylofold		RSpredict(seed)
MCC	0.723	>	0.290
Average MCC ± 95% Confidence Intervals	0.740 ± 0.196	>	0.272 ± 0.243
Sensitivity	0.703	>	0.163
Positive Predictive Value	0.751	>	0.532
Total TP	142	>	33
Total TN	14747	<	14874
Total FP	60	>	29
Total FP CONTRA	17	>	1
Total FP INCONS	30	>	28
Total FP COMP	13	>	0
Total FN	60	<	169
P-value	0.0

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

Total Scores
MCC	0.723
Average MCC ± 95% Confidence Intervals	0.740 ± 0.196
Sensitivity	0.703
Positive Predictive Value	0.751
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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
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	0.290
Average MCC ± 95% Confidence Intervals	0.272 ± 0.243
Sensitivity	0.163
Positive Predictive Value	0.532
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.14	0.60	3	4759	2	0	2	0	19
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4832	8	0	8	0	50
3RKF_A	Purine links to Rfam database...	0.84	0.75	0.95	18	847	1	1	0	0	6
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENB_A	crcB links to Rfam database...	0.34	0.20	0.60	3	467	2	0	2	0	12
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12

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