CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		CMfinder(seed)
MCC	0.584	>	0.443
Average MCC ± 95% Confidence Intervals	0.597 ± 0.114	>	0.456 ± 0.186
Sensitivity	0.546	>	0.333
Positive Predictive Value	0.630	>	0.597
Total TP	136	>	83
Total TN	33720	<	33797
Total FP	90	>	57
Total FP CONTRA	11	>	3
Total FP INCONS	69	>	53
Total FP COMP	10	>	1
Total FN	113	<	166
P-value	8.26710183075e-09

Comparison of performance of Contrafold and CMfinder(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 Contrafold and CMfinder(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 Contrafold and CMfinder(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Contrafold and CMfinder(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 Contrafold and CMfinder(seed)).

Total Scores
MCC	0.584
Average MCC ± 95% Confidence Intervals	0.597 ± 0.114
Sensitivity	0.546
Positive Predictive Value	0.630
Nr of predictions	11

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...	0.33	0.30	0.37	7	2682	13	0	12	1	16
PDB_01092	glmS links to Rfam database...	0.70	0.65	0.76	34	10108	14	2	9	3	18
RFA_00632	HDV_ribozyme links to Rfam database...	0.38	0.39	0.37	11	4065	19	0	19	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.60	0.64	0.56	18	3973	14	4	10	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...	0.68	0.56	0.83	10	2004	5	0	2	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	4	1	0	3	8
RFA_00779	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	0	2	0	8
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	0	2	0	7
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	0	8	0	10

Total Scores
MCC	0.443
Average MCC ± 95% Confidence Intervals	0.456 ± 0.186
Sensitivity	0.333
Positive Predictive Value	0.597
Nr of predictions	11

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...	0.47	0.36	0.63	5	938	3	0	3	0	9
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2688	13	0	13	0	23
PDB_01092	glmS links to Rfam database...	0.38	0.21	0.69	11	10137	6	0	5	1	41
RFA_00632	HDV_ribozyme links to Rfam database...	0.27	0.25	0.29	7	4071	17	0	17	0	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.71	0.64	0.78	18	3982	5	2	3	0	10
RFA_00769	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	2007	0	0	0	0	9
RFA_00773	Corona_pk3 links to Rfam database...	0.00	0.00	0.00	0	1949	4	0	4	0	18
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	0	2	0	7
RFA_00809	RydC links to Rfam database...	0.41	0.38	0.46	6	2132	7	1	6	0	10

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