CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		TurboFold(seed)
MCC	0.911	>	0.587
Average MCC ± 95% Confidence Intervals	0.921 ± 0.078	>	0.618 ± 0.122
Sensitivity	0.914	>	0.513
Positive Predictive Value	0.908	>	0.678
Total TP	139	>	78
Total TN	17654	<	17692
Total FP	24	<	41
Total FP CONTRA	9	>	7
Total FP INCONS	5	<	30
Total FP COMP	10	>	4
Total FN	13	<	74
P-value	0.0

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

Total Scores
MCC	0.911
Average MCC ± 95% Confidence Intervals	0.921 ± 0.078
Sensitivity	0.914
Positive Predictive Value	0.908
Nr of predictions	8

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...	0.78	0.82	0.74	23	3974	8	7	1	0	5
RFA_00767	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	4	0	0	4	0
RFA_00768	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	0	0	0	0	0
RFA_00769	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	1	1	0	0	0
RFA_00770	Corona_pk3 links to Rfam database...	0.88	0.78	1.00	14	2002	3	0	0	3	4
RFA_00773	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	4	1	0	3	0
RFA_00779	Corona_pk3 links to Rfam database...	0.97	0.94	1.00	17	1936	0	0	0	0	1
RFA_00809	RydC links to Rfam database...	0.79	0.81	0.76	13	2128	4	0	4	0	3

Total Scores
MCC	0.587
Average MCC ± 95% Confidence Intervals	0.618 ± 0.122
Sensitivity	0.513
Positive Predictive Value	0.678
Nr of predictions	8

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_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	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	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_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.