CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		Pknots
MCC	0.774	>	0.768
Average MCC ± 95% Confidence Intervals	0.760 ± 0.060	<	0.801 ± 0.106
Sensitivity	0.642	<	0.748
Positive Predictive Value	0.936	>	0.792
Total TP	219	<	255
Total TN	38743	>	38655
Total FP	17	<	90
Total FP CONTRA	5	<	18
Total FP INCONS	10	<	49
Total FP COMP	2	<	23
Total FN	122	>	86
P-value	0.453544033954

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

Total Scores
MCC	0.774
Average MCC ± 95% Confidence Intervals	0.760 ± 0.060
Sensitivity	0.642
Positive Predictive Value	0.936
Nr of predictions	16

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
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	0.768
Average MCC ± 95% Confidence Intervals	0.801 ± 0.106
Sensitivity	0.748
Positive Predictive Value	0.792
Nr of predictions	16

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...	1.00	1.00	1.00	14	932	0	0	0	0	0
PDB_00716	HDV_ribozyme links to Rfam database...	0.69	0.70	0.70	16	2678	8	0	7	1	7
PDB_00828	Purine links to Rfam database...	0.86	0.74	1.00	20	2465	2	0	0	2	7
PDB_00829	Purine links to Rfam database...	0.60	0.46	0.79	11	2264	5	0	3	2	13
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	3	0	0	3	6
PDB_01073	SAM links to Rfam database...	0.51	0.47	0.55	16	4342	14	2	11	1	18
RFA_00632	HDV_ribozyme links to Rfam database...	0.40	0.43	0.39	12	4064	19	4	15	0	16
RFA_00636	HDV_ribozyme links to Rfam database...	0.80	0.86	0.75	24	3973	8	6	2	0	4
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	3	0	0	3	0
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...	0.97	0.94	1.00	17	1999	3	0	0	3	1
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...	0.83	0.83	0.83	15	1935	4	1	2	1	3
RFA_00808	RydC links to Rfam database...	1.00	1.00	1.00	16	2000	0	0	0	0	0
RFA_00809	RydC links to Rfam database...	0.79	0.81	0.76	13	2128	4	0	4	0	3

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