CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Alterna		Murlet(seed)
MCC	0.651	>	0.486
Average MCC ± 95% Confidence Intervals	0.675 ± 0.159	>	0.472 ± 0.166
Sensitivity	0.542	>	0.313
Positive Predictive Value	0.789	>	0.765
Total TP	135	>	78
Total TN	20759	<	20828
Total FP	37	>	25
Total FP CONTRA	4	=	4
Total FP INCONS	32	>	20
Total FP COMP	1	=	1
Total FN	114	<	171
P-value	0.0

Comparison of performance of Alterna and Murlet(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 Alterna and Murlet(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 Alterna and Murlet(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Alterna and Murlet(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 Alterna and Murlet(seed)).

Total Scores
MCC	0.651
Average MCC ± 95% Confidence Intervals	0.675 ± 0.159
Sensitivity	0.542
Positive Predictive Value	0.789
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.40	0.53	8	1525	7	0	7	0	12
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.70	1.00	26	3629	0	0	0	0	11
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
3IVN_B	Purine links to Rfam database...	0.74	0.61	0.90	19	2325	2	1	1	0	12
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26

Total Scores
MCC	0.486
Average MCC ± 95% Confidence Intervals	0.472 ± 0.166
Sensitivity	0.313
Positive Predictive Value	0.765
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.52	0.27	1.00	3	403	0	0	0	0	8
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.57	0.32	1.00	12	3643	0	0	0	0	25
3GX2_A	SAM links to Rfam database...	0.59	0.35	1.00	14	4357	1	0	0	1	26
3IVN_B	Purine links to Rfam database...	0.53	0.39	0.75	12	2330	4	2	2	0	19
3LA5_A	Purine links to Rfam database...	0.58	0.41	0.82	14	2468	3	1	2	0	20
3RKF_A	Purine links to Rfam database...	0.53	0.35	0.80	12	2196	3	1	2	0	22
3SD1_A	THF links to Rfam database...	0.47	0.26	0.85	11	3903	2	0	2	0	31

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