CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		NanoFolder
MCC	0.720	>	0.328
Average MCC ± 95% Confidence Intervals	0.572 ± 0.339	>	0.445 ± 0.523
Sensitivity	0.639	>	0.402
Positive Predictive Value	0.813	>	0.272
Total TP	78	>	49
Total TN	31584	>	31500
Total FP	31	<	148
Total FP CONTRA	2	<	42
Total FP INCONS	16	<	89
Total FP COMP	13	<	17
Total FN	44	<	73
P-value	0.0

Comparison of performance of Multilign(seed) and NanoFolder. 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 Multilign(seed) and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(seed) and NanoFolder. 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 Multilign(seed) and NanoFolder).

Total Scores
MCC	0.720
Average MCC ± 95% Confidence Intervals	0.572 ± 0.339
Sensitivity	0.639
Positive Predictive Value	0.813
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00416	Hammerhead_3 links to Rfam database...	0.57	0.53	0.62	8	1472	6	1	4	1	7
RFA_00664	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	2	0	2	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00808	RydC links to Rfam database...	0.60	0.56	0.64	9	2002	5	0	5	0	7
RFA_00816	R2_retro_el links to Rfam database...	1.00	1.00	1.00	41	23179	12	0	0	12	0

Total Scores
MCC	0.328
Average MCC ± 95% Confidence Intervals	0.445 ± 0.523
Sensitivity	0.402
Positive Predictive Value	0.272
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00416	Hammerhead_3 links to Rfam database...	0.94	1.00	0.88	15	1468	6	2	0	4	0
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	978	13	0	12	1	14
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1996	24	0	20	4	18
RFA_00773	Corona_pk3 links to Rfam database...	0.93	1.00	0.86	18	1932	9	3	0	6	0
RFA_00808	RydC links to Rfam database...	0.83	1.00	0.70	16	1993	7	7	0	0	0
RFA_00816	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	23133	89	30	57	2	41

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