CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		RNAwolf
MCC	0.633	>	0.497
Average MCC ± 95% Confidence Intervals	0.640 ± 0.098	>	0.475 ± 0.083
Sensitivity	0.562	>	0.481
Positive Predictive Value	0.716	>	0.519
Total TP	131	>	112
Total TN	46901	>	46868
Total FP	57	<	133
Total FP CONTRA	11	<	26
Total FP INCONS	41	<	78
Total FP COMP	5	<	29
Total FN	102	<	121
P-value	1.75835195567e-08

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

Total Scores
MCC	0.633
Average MCC ± 95% Confidence Intervals	0.640 ± 0.098
Sensitivity	0.562
Positive Predictive Value	0.716
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00210	RNaseP_arch links to Rfam database...	0.71	0.68	0.75	44	27202	16	4	11	1	21
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_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

Total Scores
MCC	0.497
Average MCC ± 95% Confidence Intervals	0.475 ± 0.083
Sensitivity	0.481
Positive Predictive Value	0.519
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00210	RNaseP_arch links to Rfam database...	0.62	0.63	0.61	41	27194	39	9	17	13	24
RFA_00636	HDV_ribozyme links to Rfam database...	0.40	0.39	0.41	11	3978	19	1	15	3	17
RFA_00767	Corona_pk3 links to Rfam database...	0.48	0.44	0.53	8	1876	8	1	6	1	10
RFA_00768	Corona_pk3 links to Rfam database...	0.50	0.44	0.57	8	1877	8	1	5	2	10
RFA_00769	Corona_pk3 links to Rfam database...	0.41	0.44	0.38	8	1932	13	3	10	0	10
RFA_00770	Corona_pk3 links to Rfam database...	0.51	0.50	0.53	9	1999	12	2	6	4	9
RFA_00773	Corona_pk3 links to Rfam database...	0.42	0.39	0.47	7	1938	12	1	7	4	11
RFA_00779	Corona_pk3 links to Rfam database...	0.26	0.28	0.26	5	1934	14	6	8	0	13
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	2	0	0	7
RFA_00809	RydC links to Rfam database...	0.47	0.38	0.60	6	2135	6	0	4	2	10

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