CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		Fold
MCC	0.767	>	0.572
Average MCC ± 95% Confidence Intervals	0.758 ± 0.057	>	0.562 ± 0.146
Sensitivity	0.634	>	0.534
Positive Predictive Value	0.933	>	0.619
Total TP	249	>	210
Total TN	48863	>	48791
Total FP	21	<	142
Total FP CONTRA	5	<	17
Total FP INCONS	13	<	112
Total FP COMP	3	<	13
Total FN	144	<	183
P-value	2.30549897711e-08

Comparison of performance of CentroidAlifold(seed) and Fold. 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 CentroidAlifold(seed) and Fold).
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 CentroidAlifold(seed) and Fold).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and Fold. 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 CentroidAlifold(seed) and Fold).

Total Scores
MCC	0.767
Average MCC ± 95% Confidence Intervals	0.758 ± 0.057
Sensitivity	0.634
Positive Predictive Value	0.933
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...	0.80	0.64	1.00	9	937	0	0	0	0	5
PDB_00716	HDV_ribozyme links to Rfam database...	0.75	0.61	0.93	14	2686	1	0	1	0	9
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...	0.91	0.83	1.00	20	2258	0	0	0	0	4
PDB_01020	Purine links to Rfam database...	0.91	0.83	1.00	19	2259	1	0	0	1	4
PDB_01073	SAM links to Rfam database...	0.84	0.71	1.00	24	4347	1	0	0	1	10
PDB_01092	glmS links to Rfam database...	0.72	0.58	0.91	30	10120	4	0	3	1	22
RFA_00632	HDV_ribozyme links to Rfam database...	0.74	0.64	0.86	18	4074	3	2	1	0	10
RFA_00636	HDV_ribozyme links to Rfam database...	0.78	0.68	0.90	19	3984	2	2	0	0	9
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...	0.74	0.56	1.00	10	1943	0	0	0	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	2006	0	0	0	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1943	0	0	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...	0.65	0.56	0.75	9	2004	3	1	2	0	7
RFA_00809	RydC links to Rfam database...	0.43	0.38	0.50	6	2133	6	0	6	0	10

Total Scores
MCC	0.572
Average MCC ± 95% Confidence Intervals	0.562 ± 0.146
Sensitivity	0.534
Positive Predictive Value	0.619
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...	0.73	0.63	0.85	33	10114	8	0	6	2	19
RFA_00632	HDV_ribozyme links to Rfam database...	0.39	0.39	0.39	11	4067	17	2	15	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.42	0.43	0.43	12	3977	16	2	14	0	16
RFA_00767	Corona_pk3 links to Rfam database...	0.44	0.44	0.44	8	1873	10	1	9	0	10
RFA_00768	Corona_pk3 links to Rfam database...	0.45	0.44	0.47	8	1874	10	1	8	1	10
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	2001	8	0	5	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	3	1	0	2	8
RFA_00779	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2000	18	2	14	2	16
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.