CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidFold		RNASampler(seed)
MCC	0.526	>	0.526
Average MCC ± 95% Confidence Intervals	0.531 ± 0.221	>	0.497 ± 0.225
Sensitivity	0.438	>	0.389
Positive Predictive Value	0.637	<	0.715
Total TP	116	>	103
Total TN	49916	<	49954
Total FP	75	>	56
Total FP CONTRA	12	>	4
Total FP INCONS	54	>	37
Total FP COMP	9	<	15
Total FN	149	<	162
P-value	0.0

Comparison of performance of CentroidFold 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 CentroidFold and RNASampler(seed)).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for CentroidFold and RNASampler(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidFold 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 CentroidFold and RNASampler(seed)).

Total Scores
MCC	0.526
Average MCC ± 95% Confidence Intervals	0.531 ± 0.221
Sensitivity	0.438
Positive Predictive Value	0.637
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...	0.49	0.35	0.70	7	1530	3	1	2	0	13
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.23	0.21	0.25	7	12218	25	5	16	4	26
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.29	0.50	10	12383	10	0	10	0	25
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.58	0.48	0.71	20	3888	8	1	7	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11752	29	5	19	5	28

Total Scores
MCC	0.526
Average MCC ± 95% Confidence Intervals	0.497 ± 0.225
Sensitivity	0.389
Positive Predictive Value	0.715
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...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.70	0.49	1.00	18	3637	0	0	0	0	19
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.30	0.50	10	12226	13	2	8	3	23
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	12	2	6	4	23
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.60	0.38	0.94	16	3899	1	0	1	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

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