CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ProbKnot		CMfinder(seed)
MCC	0.513	>	0.443
Average MCC ± 95% Confidence Intervals	0.513 ± 0.147	>	0.456 ± 0.186
Sensitivity	0.494	>	0.333
Positive Predictive Value	0.539	<	0.597
Total TP	123	>	83
Total TN	33708	<	33797
Total FP	111	>	57
Total FP CONTRA	12	>	3
Total FP INCONS	93	>	53
Total FP COMP	6	>	1
Total FN	126	<	166
P-value	2.12160100812e-08

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

Total Scores
MCC	0.513
Average MCC ± 95% Confidence Intervals	0.513 ± 0.147
Sensitivity	0.494
Positive Predictive Value	0.539
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...	0.78	0.79	0.79	11	932	3	0	3	0	3
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2680	22	0	21	1	23
PDB_01092	glmS links to Rfam database...	0.73	0.63	0.85	33	10114	8	1	5	2	19
RFA_00632	HDV_ribozyme links to Rfam database...	0.40	0.39	0.41	11	4068	16	0	16	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.44	0.46	0.43	13	3975	17	0	17	0	15
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...	0.59	0.56	0.63	10	2000	9	0	6	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	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...	0.65	0.56	0.75	9	2004	3	0	3	0	7
RFA_00809	RydC links to Rfam database...	0.35	0.38	0.33	6	2127	12	1	11	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.