CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RSpredict(seed)
MCC	0.485	>	0.479
Average MCC ± 95% Confidence Intervals	0.399 ± 0.173	<	0.495 ± 0.104
Sensitivity	0.386	<	0.423
Positive Predictive Value	0.619	>	0.552
Total TP	83	<	91
Total TN	22737	>	22706
Total FP	52	<	80
Total FP CONTRA	6	<	28
Total FP INCONS	45	<	46
Total FP COMP	1	<	6
Total FN	132	>	124
P-value	0.0114155930811

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

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	0.479
Average MCC ± 95% Confidence Intervals	0.495 ± 0.104
Sensitivity	0.423
Positive Predictive Value	0.552
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...	0.63	0.40	1.00	6	1479	1	0	0	1	9
RFA_00654	Vimentin3 links to Rfam database...	0.35	0.28	0.45	5	2404	6	0	6	0	13
RFA_00658	Hammerhead_1 links to Rfam database...	0.64	0.57	0.73	8	1117	4	0	3	1	6
RFA_00664	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	980	4	0	3	1	7
RFA_00708	Hammerhead_1 links to Rfam database...	0.75	0.57	1.00	8	1027	1	0	0	1	6
RFA_00767	Corona_pk3 links to Rfam database...	0.19	0.17	0.23	3	1878	10	3	7	0	15
RFA_00768	Corona_pk3 links to Rfam database...	0.19	0.17	0.23	3	1878	10	3	7	0	15
RFA_00769	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	4	2	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.54	0.56	0.53	10	1997	9	6	3	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.50	0.50	0.50	9	1935	9	6	3	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.50	0.50	0.50	9	1935	9	6	3	0	9
RFA_00808	RydC links to Rfam database...	0.60	0.50	0.73	8	2005	4	0	3	1	8
RFA_00809	RydC links to Rfam database...	0.37	0.31	0.45	5	2134	7	0	6	1	11

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