CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		MCFold
MCC	0.485	>	0.359
Average MCC ± 95% Confidence Intervals	0.399 ± 0.173	>	0.381 ± 0.173
Sensitivity	0.386	<	0.419
Positive Predictive Value	0.619	>	0.319
Total TP	83	<	90
Total TN	22737	>	22589
Total FP	52	<	229
Total FP CONTRA	6	<	32
Total FP INCONS	45	<	160
Total FP COMP	1	<	37
Total FN	132	>	125
P-value	2.06323189071e-08

Comparison of performance of Multilign(seed) and MCFold. 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 Multilign(seed) and MCFold).
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 Multilign(seed) and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(seed) and MCFold. 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 Multilign(seed) and MCFold).

Total Scores
MCC	0.485
Average MCC ± 95% Confidence Intervals	0.399 ± 0.173
Sensitivity	0.386
Positive Predictive Value	0.619
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00416	Hammerhead_3 links to Rfam database...	0.57	0.53	0.62	8	1472	6	1	4	1	7
RFA_00654	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2414	1	0	1	0	18
RFA_00658	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00664	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	0	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1876	5	0	5	0	8
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...	0.68	0.56	0.83	10	2004	2	0	2	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1938	5	0	5	0	8
RFA_00808	RydC links to Rfam database...	0.60	0.56	0.64	9	2002	5	0	5	0	7
RFA_00809	RydC links to Rfam database...	0.37	0.38	0.38	6	2129	10	1	9	0	10

Total Scores
MCC	0.359
Average MCC ± 95% Confidence Intervals	0.381 ± 0.173
Sensitivity	0.419
Positive Predictive Value	0.319
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	9	0	0	9	0
RFA_00654	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2386	29	4	25	0	18
RFA_00658	Hammerhead_1 links to Rfam database...	0.62	0.64	0.60	9	1113	10	0	6	4	5
RFA_00664	Hammerhead_1 links to Rfam database...	-0.02	0.00	0.00	0	974	16	0	16	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.64	0.64	0.64	9	1021	10	0	5	5	5
RFA_00767	Corona_pk3 links to Rfam database...	0.36	0.44	0.31	8	1865	19	3	15	1	10
RFA_00768	Corona_pk3 links to Rfam database...	0.36	0.44	0.31	8	1865	19	3	15	1	10
RFA_00769	Corona_pk3 links to Rfam database...	0.45	0.50	0.41	9	1931	18	2	11	5	9
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1992	29	2	22	5	18
RFA_00773	Corona_pk3 links to Rfam database...	0.43	0.50	0.38	9	1929	16	4	11	1	9
RFA_00779	Corona_pk3 links to Rfam database...	0.45	0.56	0.37	10	1926	17	7	10	0	8
RFA_00808	RydC links to Rfam database...	0.39	0.44	0.35	7	1996	19	1	12	6	9
RFA_00809	RydC links to Rfam database...	0.30	0.38	0.25	6	2121	18	6	12	0	10

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