CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Multilign(seed)		CentroidHomfold‑LAST
MCC	0.734	>	0.710
Average MCC ± 95% Confidence Intervals	0.740 ± 0.146	>	0.679 ± 0.128
Sensitivity	0.733	>	0.608
Positive Predictive Value	0.737	<	0.831
Total TP	493	>	409
Total TN	383507	<	383684
Total FP	263	>	113
Total FP CONTRA	42	>	17
Total FP INCONS	134	>	66
Total FP COMP	87	>	30
Total FN	180	<	264
P-value	1.50834591464e-08

Comparison of performance of Multilign(seed) and CentroidHomfold-LAST. 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 CentroidHomfold‑LAST).
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 CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(seed) and CentroidHomfold-LAST. 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 CentroidHomfold‑LAST).

Total Scores
MCC	0.734
Average MCC ± 95% Confidence Intervals	0.740 ± 0.146
Sensitivity	0.733
Positive Predictive Value	0.737
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00619	-	0.37	0.41	0.34	16	22744	36	12	19	5	23
RFA_00626	rne5 links to Rfam database...	0.90	0.85	0.95	74	56538	20	0	4	16	13
RFA_00628	rne5 links to Rfam database...	0.92	0.88	0.95	76	57211	18	0	4	14	10
RFA_00630	rne5 links to Rfam database...	0.83	0.80	0.86	70	56872	29	0	11	18	17
RFA_00816	R2_retro_el links to Rfam database...	1.00	1.00	1.00	41	23179	12	0	0	12	0
RFA_00817	R2_retro_el links to Rfam database...	0.77	0.78	0.76	32	21903	13	5	5	3	9
RFA_00818	R2_retro_el links to Rfam database...	0.85	0.80	0.89	33	20264	12	1	3	8	8
SRP_00241	Plant_SRP links to Rfam database...	0.48	0.50	0.46	41	45967	50	15	33	2	41
SRP_00331	Metazoa_SRP links to Rfam database...	0.69	0.69	0.70	60	37589	29	2	24	3	27
SRP_00340	Metazoa_SRP links to Rfam database...	0.59	0.61	0.57	50	41240	44	7	31	6	32

Total Scores
MCC	0.710
Average MCC ± 95% Confidence Intervals	0.679 ± 0.128
Sensitivity	0.608
Positive Predictive Value	0.831
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00619	-	0.29	0.23	0.36	9	22766	23	3	13	7	30
RFA_00626	rne5 links to Rfam database...	0.85	0.79	0.92	69	56541	13	1	5	7	18
RFA_00628	rne5 links to Rfam database...	0.86	0.78	0.94	67	57220	7	1	3	3	19
RFA_00630	rne5 links to Rfam database...	0.87	0.83	0.92	72	56875	10	1	5	4	15
RFA_00816	R2_retro_el links to Rfam database...	0.80	0.63	1.00	26	23194	1	0	0	1	15
RFA_00817	R2_retro_el links to Rfam database...	0.68	0.59	0.80	24	21915	9	2	4	3	17
RFA_00818	R2_retro_el links to Rfam database...	0.57	0.54	0.61	22	20265	18	8	6	4	19
SRP_00241	Plant_SRP links to Rfam database...	0.65	0.51	0.82	42	46005	10	0	9	1	40
SRP_00331	Metazoa_SRP links to Rfam database...	0.60	0.53	0.69	46	37608	21	1	20	0	41
SRP_00340	Metazoa_SRP links to Rfam database...	0.61	0.39	0.97	32	41295	1	0	1	0	50

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