CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Afold		RNASampler(seed)
MCC	0.647	>	0.627
Average MCC ± 95% Confidence Intervals	0.664 ± 0.325	>	0.583 ± 0.380
Sensitivity	0.672	>	0.555
Positive Predictive Value	0.630	<	0.717
Total TP	92	>	76
Total TN	12931	<	12971
Total FP	87	>	43
Total FP CONTRA	17	>	9
Total FP INCONS	37	>	21
Total FP COMP	33	>	13
Total FN	45	<	61
P-value	0.0

Comparison of performance of Afold and RNASampler(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 Afold and RNASampler(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and RNASampler(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 Afold and RNASampler(seed)).

Total Scores
MCC	0.647
Average MCC ± 95% Confidence Intervals	0.664 ± 0.325
Sensitivity	0.672
Positive Predictive Value	0.630
Nr of predictions	6

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	6	0	5	1	7
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15

Total Scores
MCC	0.627
Average MCC ± 95% Confidence Intervals	0.583 ± 0.380
Sensitivity	0.555
Positive Predictive Value	0.717
Nr of predictions	6

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	518	10	0	10	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.77	0.60	1.00	18	1482	0	0	0	0	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.50	0.58	11	4745	13	5	3	5	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.40	0.40	0.40	8	4496	20	4	8	8	12

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