CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		RDfolder
MCC	0.641	>	0.561
Average MCC ± 95% Confidence Intervals	0.633 ± 0.095	>	0.584 ± 0.145
Sensitivity	0.562	>	0.481
Positive Predictive Value	0.736	>	0.663
Total TP	131	>	112
Total TN	27387	<	27396
Total FP	48	<	59
Total FP CONTRA	20	>	12
Total FP INCONS	27	<	45
Total FP COMP	1	<	2
Total FN	102	<	121
P-value	1.84361416392e-08

Comparison of performance of RNASampler(seed) and RDfolder. 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 RNASampler(seed) and RDfolder).
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 RNASampler(seed) and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(seed) and RDfolder. 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 RNASampler(seed) and RDfolder).

Total Scores
MCC	0.641
Average MCC ± 95% Confidence Intervals	0.633 ± 0.095
Sensitivity	0.562
Positive Predictive Value	0.736
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00716	HDV_ribozyme links to Rfam database...	0.50	0.39	0.64	9	2687	6	0	5	1	14
RFA_00632	HDV_ribozyme links to Rfam database...	0.78	0.68	0.90	19	4074	2	1	1	0	9
RFA_00636	HDV_ribozyme links to Rfam database...	0.85	0.75	0.95	21	3983	1	1	0	0	7
RFA_00767	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	3	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	3	0	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.52	0.39	0.70	7	2006	3	3	0	0	11
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.50	0.69	9	1940	4	4	0	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	3	0	0	8
RFA_00808	RydC links to Rfam database...	0.58	0.56	0.60	9	2001	6	0	6	0	7
RFA_00809	RydC links to Rfam database...	0.36	0.38	0.35	6	2128	11	1	10	0	10

Total Scores
MCC	0.561
Average MCC ± 95% Confidence Intervals	0.584 ± 0.145
Sensitivity	0.481
Positive Predictive Value	0.663
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2684	18	1	16	1	23
RFA_00632	HDV_ribozyme links to Rfam database...	0.62	0.54	0.71	15	4074	6	1	5	0	13
RFA_00636	HDV_ribozyme links to Rfam database...	0.65	0.64	0.67	18	3978	9	3	6	0	10
RFA_00767	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1882	0	0	0	0	9
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...	0.50	0.50	0.50	9	1935	9	4	5	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.47	0.39	0.58	7	2004	5	1	4	0	11
RFA_00773	Corona_pk3 links to Rfam database...	0.67	0.50	0.90	9	1943	1	1	0	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	3	0	2	1	7
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	1	7	0	10

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