CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidHomfold‑LAST		RDfolder
MCC	0.681	>	0.423
Average MCC ± 95% Confidence Intervals	0.592 ± 0.388	>	0.370 ± 0.299
Sensitivity	0.567	>	0.355
Positive Predictive Value	0.833	>	0.532
Total TP	80	>	50
Total TN	5647	<	5649
Total FP	17	<	45
Total FP CONTRA	2	<	10
Total FP INCONS	14	<	34
Total FP COMP	1	=	1
Total FN	61	<	91
P-value	0.0

Comparison of performance of CentroidHomfold-LAST 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 CentroidHomfold‑LAST and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST 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 CentroidHomfold‑LAST and RDfolder).

Total Scores
MCC	0.681
Average MCC ± 95% Confidence Intervals	0.592 ± 0.388
Sensitivity	0.567
Positive Predictive Value	0.833
Nr of predictions	7

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	517	11	0	11	0	18
3J0L_a	-	-0.01	0.00	0.00	0	408	3	1	2	0	11
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.77	0.66	0.90	19	1512	2	1	1	0	10
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	1	0	0	1	8
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4

Total Scores
MCC	0.423
Average MCC ± 95% Confidence Intervals	0.370 ± 0.299
Sensitivity	0.355
Positive Predictive Value	0.532
Nr of predictions	7

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	514	14	3	11	0	18
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	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...	0.35	0.24	0.54	7	1520	6	1	5	0	22
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...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9

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