CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Pknots		Murlet(seed)
MCC	0.803	>	0.432
Average MCC ± 95% Confidence Intervals	0.833 ± 0.128	>	0.444 ± 0.103
Sensitivity	0.820	>	0.283
Positive Predictive Value	0.789	>	0.667
Total TP	191	>	66
Total TN	27323	<	27466
Total FP	66	>	35
Total FP CONTRA	16	>	0
Total FP INCONS	35	>	33
Total FP COMP	15	>	2
Total FN	42	<	167
P-value	1.59816551561e-08

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

Total Scores
MCC	0.803
Average MCC ± 95% Confidence Intervals	0.833 ± 0.128
Sensitivity	0.820
Positive Predictive Value	0.789
Nr of predictions	12

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
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

Total Scores
MCC	0.432
Average MCC ± 95% Confidence Intervals	0.444 ± 0.103
Sensitivity	0.283
Positive Predictive Value	0.667
Nr of predictions	12

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...	0.53	0.29	1.00	4	942	2	0	0	2	10
PDB_00716	HDV_ribozyme links to Rfam database...	0.23	0.13	0.43	3	2694	4	0	4	0	20
RFA_00632	HDV_ribozyme links to Rfam database...	0.21	0.11	0.43	3	4088	4	0	4	0	25
RFA_00636	HDV_ribozyme links to Rfam database...	0.21	0.11	0.43	3	3998	4	0	4	0	25
RFA_00767	Corona_pk3 links to Rfam database...	0.47	0.33	0.67	6	1882	3	0	3	0	12
RFA_00768	Corona_pk3 links to Rfam database...	0.41	0.28	0.63	5	1883	3	0	3	0	13
RFA_00769	Corona_pk3 links to Rfam database...	0.57	0.44	0.73	8	1942	3	0	3	0	10
RFA_00770	Corona_pk3 links to Rfam database...	0.57	0.44	0.73	8	2005	3	0	3	0	10
RFA_00773	Corona_pk3 links to Rfam database...	0.41	0.28	0.63	5	1945	3	0	3	0	13
RFA_00779	Corona_pk3 links to Rfam database...	0.47	0.33	0.67	6	1944	3	0	3	0	12
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.50	0.38	0.67	6	2136	3	0	3	0	10

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