CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CMfinder(seed)		TurboFold(seed)
MCC	0.589	>	0.569
Average MCC ± 95% Confidence Intervals	0.558 ± 0.250	<	0.600 ± 0.137
Sensitivity	0.455	<	0.508
Positive Predictive Value	0.769	>	0.644
Total TP	60	<	67
Total TN	15963	>	15937
Total FP	18	<	41
Total FP CONTRA	3	<	7
Total FP INCONS	15	<	30
Total FP COMP	0	<	4
Total FN	72	>	65
P-value	0.0

Comparison of performance of CMfinder(seed) and TurboFold(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 CMfinder(seed) and TurboFold(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 CMfinder(seed) and TurboFold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CMfinder(seed) and TurboFold(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 CMfinder(seed) and TurboFold(seed)).

Total Scores
MCC	0.589
Average MCC ± 95% Confidence Intervals	0.558 ± 0.250
Sensitivity	0.455
Positive Predictive Value	0.769
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00636	HDV_ribozyme links to Rfam database...	0.71	0.64	0.78	18	3982	5	2	3	0	10
RFA_00769	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	2007	0	0	0	0	9
RFA_00773	Corona_pk3 links to Rfam database...	0.00	0.00	0.00	0	1949	4	0	4	0	18
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	0	2	0	7
RFA_00809	RydC links to Rfam database...	0.41	0.38	0.46	6	2132	7	1	6	0	10

Total Scores
MCC	0.569
Average MCC ± 95% Confidence Intervals	0.600 ± 0.137
Sensitivity	0.508
Positive Predictive Value	0.644
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00636	HDV_ribozyme links to Rfam database...	0.42	0.43	0.43	12	3977	16	2	14	0	16
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	5	0	2	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	2	1	0	1	8
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	1	0	1	0	8
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.38	0.38	0.40	6	2130	9	1	8	0	10

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