CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		MaxExpect
MCC	0.729	>	0.588
Average MCC ± 95% Confidence Intervals	0.718 ± 0.056	>	0.590 ± 0.112
Sensitivity	0.649	>	0.549
Positive Predictive Value	0.824	>	0.636
Total TP	285	>	241
Total TN	54590	>	54557
Total FP	70	<	146
Total FP CONTRA	33	>	21
Total FP INCONS	28	<	117
Total FP COMP	9	>	8
Total FN	154	<	198
P-value	3.24519439238e-08

Comparison of performance of PETfold_pre2.0(seed) and MaxExpect. 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 PETfold_pre2.0(seed) and MaxExpect).
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 PETfold_pre2.0(seed) and MaxExpect).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and MaxExpect. 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 PETfold_pre2.0(seed) and MaxExpect).

Total Scores
MCC	0.729
Average MCC ± 95% Confidence Intervals	0.718 ± 0.056
Sensitivity	0.649
Positive Predictive Value	0.824
Nr of predictions	19

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...	0.80	0.64	1.00	9	937	0	0	0	0	5
PDB_00571	tRNA links to Rfam database...	0.85	0.80	0.91	20	3299	2	2	0	0	5
PDB_00716	HDV_ribozyme links to Rfam database...	0.68	0.57	0.81	13	2685	3	0	3	0	10
PDB_00828	Purine links to Rfam database...	0.84	0.78	0.91	21	2462	3	2	0	1	6
PDB_00829	Purine links to Rfam database...	0.87	0.83	0.91	20	2256	3	2	0	1	4
PDB_01009	tRNA links to Rfam database...	0.93	0.90	0.95	19	2465	3	0	1	2	2
PDB_01020	Purine links to Rfam database...	0.86	0.83	0.90	19	2257	4	2	0	2	4
PDB_01073	SAM links to Rfam database...	0.77	0.68	0.88	23	4345	4	2	1	1	11
PDB_01092	glmS links to Rfam database...	0.68	0.56	0.83	29	10118	8	0	6	2	23
RFA_00632	HDV_ribozyme links to Rfam database...	0.69	0.64	0.75	18	4071	6	2	4	0	10
RFA_00636	HDV_ribozyme links to Rfam database...	0.73	0.68	0.79	19	3981	5	2	3	0	9
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	3	1	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	3	1	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	2002	4	3	1	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00808	RydC links to Rfam database...	0.71	0.56	0.90	9	2006	1	1	0	0	7
RFA_00809	RydC links to Rfam database...	0.47	0.38	0.60	6	2135	4	0	4	0	10

Total Scores
MCC	0.588
Average MCC ± 95% Confidence Intervals	0.590 ± 0.112
Sensitivity	0.549
Positive Predictive Value	0.636
Nr of predictions	19

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_00571	tRNA links to Rfam database...	0.42	0.36	0.50	9	3303	9	2	7	0	16
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_01009	tRNA links to Rfam database...	0.51	0.57	0.46	12	2459	14	5	9	0	9
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

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