CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		ContextFold
MCC	0.575	>	0.566
Average MCC ± 95% Confidence Intervals	0.578 ± 0.076	>	0.564 ± 0.060
Sensitivity	0.536	>	0.514
Positive Predictive Value	0.625	<	0.632
Total TP	75	>	72
Total TN	15698	<	15704
Total FP	45	>	43
Total FP CONTRA	5	<	14
Total FP INCONS	40	>	28
Total FP COMP	0	<	1
Total FN	65	<	68
P-value	0.0

Comparison of performance of Multilign(seed) and ContextFold. 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 Multilign(seed) and ContextFold).
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 Multilign(seed) and ContextFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(seed) and ContextFold. 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 Multilign(seed) and ContextFold).

Total Scores
MCC	0.575
Average MCC ± 95% Confidence Intervals	0.578 ± 0.076
Sensitivity	0.536
Positive Predictive Value	0.625
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	0	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1876	5	0	5	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	2	0	2	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1938	5	0	5	0	8
RFA_00808	RydC links to Rfam database...	0.60	0.56	0.64	9	2002	5	0	5	0	7
RFA_00809	RydC links to Rfam database...	0.37	0.38	0.38	6	2129	10	1	9	0	10

Total Scores
MCC	0.566
Average MCC ± 95% Confidence Intervals	0.564 ± 0.060
Sensitivity	0.514
Positive Predictive Value	0.632
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00767	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1875	6	3	3	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1876	5	2	3	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	4	4	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	2001	5	2	3	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1938	5	2	3	0	8
RFA_00808	RydC links to Rfam database...	0.58	0.44	0.78	7	2007	2	0	2	0	9
RFA_00809	RydC links to Rfam database...	0.39	0.31	0.50	5	2135	6	0	5	1	11

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