CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		Afold
MCC	0.588	>	0.469
Average MCC ± 95% Confidence Intervals	0.623 ± 0.125	>	0.478 ± 0.193
Sensitivity	0.513	>	0.440
Positive Predictive Value	0.681	>	0.508
Total TP	77	>	66
Total TN	17757	>	17740
Total FP	40	<	79
Total FP CONTRA	7	<	10
Total FP INCONS	29	<	54
Total FP COMP	4	<	15
Total FN	73	<	84
P-value	0.0

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

Total Scores
MCC	0.588
Average MCC ± 95% Confidence Intervals	0.623 ± 0.125
Sensitivity	0.513
Positive Predictive Value	0.681
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_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	0.469
Average MCC ± 95% Confidence Intervals	0.478 ± 0.193
Sensitivity	0.440
Positive Predictive Value	0.508
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	17	2	14	1	16
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	5	0	4	1	8
RFA_00768	Corona_pk3 links to Rfam database...	0.48	0.44	0.53	8	1876	8	1	6	1	10
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	10	3	5	2	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	6	0	2	4	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	5	1	0	4	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	16	2	13	1	16
RFA_00809	RydC links to Rfam database...	0.36	0.38	0.35	6	2128	12	1	10	1	10

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