CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Cylofold		RDfolder
MCC	0.699	>	0.435
Average MCC ± 95% Confidence Intervals	0.679 ± 0.218	>	0.389 ± 0.217
Sensitivity	0.668	>	0.378
Positive Predictive Value	0.746	>	0.525
Total TP	129	>	73
Total TN	8124	<	8158
Total FP	46	<	67
Total FP CONTRA	10	<	13
Total FP INCONS	34	<	53
Total FP COMP	2	>	1
Total FN	64	<	120
P-value	0.0

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

Total Scores
MCC	0.699
Average MCC ± 95% Confidence Intervals	0.679 ± 0.218
Sensitivity	0.668
Positive Predictive Value	0.746
Nr of predictions	9

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
3ADB_C	-	0.84	0.82	0.87	27	1788	4	0	4	0	6
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
3NKB_B	-	0.46	0.42	0.53	8	720	7	0	7	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...	0.71	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	0.435
Average MCC ± 95% Confidence Intervals	0.389 ± 0.217
Sensitivity	0.378
Positive Predictive Value	0.525
Nr of predictions	9

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
3ADB_C	-	0.48	0.45	0.54	15	1791	13	1	12	0	18
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
3NKB_B	-	0.43	0.42	0.47	8	718	9	2	7	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.