CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Contrafold		Carnac(seed)
MCC	0.582	>	0.582
Average MCC ± 95% Confidence Intervals	0.597 ± 0.101	>	0.456 ± 0.229
Sensitivity	0.540	>	0.354
Positive Predictive Value	0.634	<	0.962
Total TP	154	>	101
Total TN	37475	<	37613
Total FP	101	>	5
Total FP CONTRA	12	>	3
Total FP INCONS	77	>	1
Total FP COMP	12	>	1
Total FN	131	<	184
P-value	0.00256031511034

Comparison of performance of Contrafold and Carnac(seed). 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 Contrafold and Carnac(seed)).
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 Contrafold and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Contrafold and Carnac(seed). 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 Contrafold and Carnac(seed)).

Total Scores
MCC	0.582
Average MCC ± 95% Confidence Intervals	0.597 ± 0.101
Sensitivity	0.540
Positive Predictive Value	0.634
Nr of predictions	13

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...	0.33	0.30	0.37	7	2682	13	0	12	1	16
PDB_01092	glmS links to Rfam database...	0.70	0.65	0.76	34	10108	14	2	9	3	18
RFA_00632	HDV_ribozyme links to Rfam database...	0.38	0.39	0.37	11	4065	19	0	19	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.60	0.64	0.56	18	3973	14	4	10	0	10
RFA_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	2	0	0	2	8
RFA_00768	Corona_pk3 links to Rfam database...	0.45	0.44	0.47	8	1874	9	1	8	0	10
RFA_00769	Corona_pk3 links to Rfam database...	0.54	0.56	0.53	10	1934	9	4	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	4	1	0	3	8
RFA_00779	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	0	2	0	8
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	0	2	0	7
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	0	8	0	10

Total Scores
MCC	0.582
Average MCC ± 95% Confidence Intervals	0.456 ± 0.229
Sensitivity	0.354
Positive Predictive Value	0.962
Nr of predictions	13

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...	0.00	0.00	0.00	0	2701	0	0	0	0	23
PDB_01092	glmS links to Rfam database...	0.77	0.63	0.94	33	10118	3	1	1	1	19
RFA_00632	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	4095	0	0	0	0	28
RFA_00636	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	4005	0	0	0	0	28
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...	0.71	0.56	0.91	10	1942	1	1	0	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.62	0.39	1.00	7	2009	0	0	0	0	11
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	1	1	0	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1943	0	0	0	0	8
RFA_00808	RydC links to Rfam database...	0.00	0.00	0.00	0	2016	0	0	0	0	16
RFA_00809	RydC links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	16

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