CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MaxExpect		Mastr(seed)
MCC	0.603	>	0.341
Average MCC ± 95% Confidence Intervals	0.605 ± 0.124	>	0.295 ± 0.170
Sensitivity	0.560	>	0.176
Positive Predictive Value	0.657	<	0.670
Total TP	220	>	69
Total TN	48795	<	49027
Total FP	123	>	37
Total FP CONTRA	14	>	5
Total FP INCONS	101	>	29
Total FP COMP	8	>	3
Total FN	173	<	324
P-value	3.05041766982e-08

Comparison of performance of MaxExpect and Mastr(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 MaxExpect and Mastr(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 MaxExpect and Mastr(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for MaxExpect and Mastr(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 MaxExpect and Mastr(seed)).

Total Scores
MCC	0.603
Average MCC ± 95% Confidence Intervals	0.605 ± 0.124
Sensitivity	0.560
Positive Predictive Value	0.657
Nr of predictions	17

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	2678	24	1	22	1	23
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01073	SAM links to Rfam database...	0.86	0.74	1.00	25	4346	1	0	0	1	9
PDB_01092	glmS links to Rfam database...	0.75	0.63	0.89	33	10116	6	0	4	2	19
RFA_00632	HDV_ribozyme links to Rfam database...	0.34	0.36	0.33	10	4065	20	2	18	0	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.41	0.43	0.40	12	3975	18	2	16	0	16
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	0	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.47	0.44	0.50	8	1875	8	1	7	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...	0.63	0.56	0.71	10	2002	7	0	4	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1938	5	2	3	0	8
RFA_00808	RydC links to Rfam database...	0.62	0.56	0.69	9	2003	4	0	4	0	7
RFA_00809	RydC links to Rfam database...	0.37	0.38	0.38	6	2129	10	1	9	0	10

Total Scores
MCC	0.341
Average MCC ± 95% Confidence Intervals	0.295 ± 0.170
Sensitivity	0.176
Positive Predictive Value	0.670
Nr of predictions	17

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...	0.60	0.43	0.86	6	939	2	0	1	1	8
PDB_00716	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	23
PDB_00828	Purine links to Rfam database...	0.00	0.00	0.00	0	2485	0	0	0	0	27
PDB_00829	Purine links to Rfam database...	0.00	0.00	0.00	0	2278	0	0	0	0	24
PDB_01020	Purine links to Rfam database...	0.00	0.00	0.00	0	2278	0	0	0	0	23
PDB_01073	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	34
PDB_01092	glmS links to Rfam database...	0.00	0.00	0.00	0	10153	0	0	0	0	52
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...	0.67	0.50	0.90	9	1881	1	0	1	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...	0.64	0.50	0.82	9	1942	2	1	1	0	9
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...	0.64	0.50	0.82	9	1942	2	1	1	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	0	3	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	17	2	13	2	16
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.