CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Cylofold		Carnac(seed)
MCC	0.831	>	0.550
Average MCC ± 95% Confidence Intervals	0.852 ± 0.102	>	0.469 ± 0.253
Sensitivity	0.834	>	0.313
Positive Predictive Value	0.830	<	0.971
Total TP	181	>	68
Total TN	25331	<	25479
Total FP	48	>	2
Total FP CONTRA	11	>	2
Total FP INCONS	26	>	0
Total FP COMP	11	>	0
Total FN	36	<	149
P-value	9.54892753461e-09

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

Total Scores
MCC	0.831
Average MCC ± 95% Confidence Intervals	0.852 ± 0.102
Sensitivity	0.834
Positive Predictive Value	0.830
Nr of predictions	11

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...	0.78	0.79	0.79	11	932	3	0	3	0	3
PDB_00716	HDV_ribozyme links to Rfam database...	0.68	0.70	0.67	16	2677	9	0	8	1	7
RFA_00632	HDV_ribozyme links to Rfam database...	0.54	0.54	0.56	15	4068	12	2	10	0	13
RFA_00636	HDV_ribozyme links to Rfam database...	0.78	0.82	0.74	23	3974	8	7	1	0	5
RFA_00767	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	4	0	0	4	0
RFA_00768	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	0	0	0	0	0
RFA_00769	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	1	1	0	0	0
RFA_00770	Corona_pk3 links to Rfam database...	0.88	0.78	1.00	14	2002	3	0	0	3	4
RFA_00773	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	4	1	0	3	0
RFA_00779	Corona_pk3 links to Rfam database...	0.97	0.94	1.00	17	1936	0	0	0	0	1
RFA_00809	RydC links to Rfam database...	0.79	0.81	0.76	13	2128	4	0	4	0	3

Total Scores
MCC	0.550
Average MCC ± 95% Confidence Intervals	0.469 ± 0.253
Sensitivity	0.313
Positive Predictive Value	0.971
Nr of predictions	11

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
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_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.