CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	ProbKnot		RDfolder
MCC	0.606	>	0.424
Average MCC ± 95% Confidence Intervals	0.590 ± 0.231	>	0.377 ± 0.251
Sensitivity	0.606	>	0.363
Positive Predictive Value	0.626	>	0.523
Total TP	97	>	58
Total TN	6323	<	6367
Total FP	61	>	54
Total FP CONTRA	20	>	12
Total FP INCONS	38	<	41
Total FP COMP	3	>	1
Total FN	63	<	102
P-value	0.0

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

Total Scores
MCC	0.606
Average MCC ± 95% Confidence Intervals	0.590 ± 0.231
Sensitivity	0.606
Positive Predictive Value	0.626
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	513	15	3	12	0	18
3J0L_a	-	0.60	0.64	0.58	7	399	6	4	1	1	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7

Total Scores
MCC	0.424
Average MCC ± 95% Confidence Intervals	0.377 ± 0.251
Sensitivity	0.363
Positive Predictive Value	0.523
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	514	14	3	11	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.