CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	McQFold		CentroidHomfold‑LAST
MCC	0.687	>	0.635
Average MCC ± 95% Confidence Intervals	0.689 ± 0.247	>	0.574 ± 0.299
Sensitivity	0.689	>	0.552
Positive Predictive Value	0.696	<	0.743
Total TP	126	>	101
Total TN	11354	<	11399
Total FP	65	>	50
Total FP CONTRA	20	>	10
Total FP INCONS	35	>	25
Total FP COMP	10	<	15
Total FN	57	<	82
P-value	0.0

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

Total Scores
MCC	0.687
Average MCC ± 95% Confidence Intervals	0.689 ± 0.247
Sensitivity	0.689
Positive Predictive Value	0.696
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
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
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...	0.82	0.83	0.83	24	1504	5	1	4	0	5
3U4M_B	-	0.95	0.91	1.00	20	1256	2	0	0	2	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	33	11	16	6	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
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	0.635
Average MCC ± 95% Confidence Intervals	0.574 ± 0.299
Sensitivity	0.552
Positive Predictive Value	0.743
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	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
3U4M_B	-	0.78	0.73	0.84	16	1257	4	0	3	1	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	29	8	8	13	15
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

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