CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(seed)		Afold
MCC	0.664	>	0.480
Average MCC ± 95% Confidence Intervals	0.662 ± 0.072	>	0.486 ± 0.230
Sensitivity	0.533	>	0.443
Positive Predictive Value	0.833	>	0.529
Total TP	65	>	54
Total TN	13787	>	13763
Total FP	13	<	62
Total FP CONTRA	5	<	8
Total FP INCONS	8	<	40
Total FP COMP	0	<	14
Total FN	57	<	68
P-value	0.0

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

Total Scores
MCC	0.664
Average MCC ± 95% Confidence Intervals	0.662 ± 0.072
Sensitivity	0.533
Positive Predictive Value	0.833
Nr of predictions	7

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...	0.68	0.56	0.83	10	1879	2	1	1	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1879	2	1	1	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	1	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	2	1	1	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	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...	0.50	0.38	0.67	6	2136	3	0	3	0	10

Total Scores
MCC	0.480
Average MCC ± 95% Confidence Intervals	0.486 ± 0.230
Sensitivity	0.443
Positive Predictive Value	0.529
Nr of predictions	7

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	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.