CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		MaxExpect
MCC	0.734	>	0.571
Average MCC ± 95% Confidence Intervals	0.740 ± 0.146	>	0.540 ± 0.177
Sensitivity	0.733	>	0.596
Positive Predictive Value	0.737	>	0.548
Total TP	493	>	401
Total TN	383507	>	383444
Total FP	263	<	409
Total FP CONTRA	42	<	92
Total FP INCONS	134	<	239
Total FP COMP	87	>	78
Total FN	180	<	272
P-value	1.38194587311e-08

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

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	0.571
Average MCC ± 95% Confidence Intervals	0.540 ± 0.177
Sensitivity	0.596
Positive Predictive Value	0.548
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	0.33	0.25	13	22739	51	13	26	12	26
RFA_00626	rne5 links to Rfam database...	0.88	0.84	0.92	73	56537	23	2	4	17	14
RFA_00628	rne5 links to Rfam database...	0.91	0.88	0.94	76	57210	25	0	5	20	10
RFA_00630	rne5 links to Rfam database...	0.66	0.66	0.66	57	56867	44	7	22	15	30
RFA_00816	R2_retro_el links to Rfam database...	0.63	0.66	0.60	27	23175	24	11	7	6	14
RFA_00817	R2_retro_el links to Rfam database...	0.10	0.12	0.08	5	21883	57	17	40	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.48	0.54	0.43	22	20250	30	12	17	1	19
SRP_00241	Plant_SRP links to Rfam database...	0.44	0.48	0.41	39	45961	58	14	42	2	43
SRP_00331	Metazoa_SRP links to Rfam database...	0.52	0.53	0.52	46	37586	45	7	36	2	41
SRP_00340	Metazoa_SRP links to Rfam database...	0.49	0.52	0.47	43	41236	52	9	40	3	39

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