CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		Vsfold4
MCC	0.734	>	0.167
Average MCC ± 95% Confidence Intervals	0.740 ± 0.146	>	0.153 ± 0.061
Sensitivity	0.733	>	0.160
Positive Predictive Value	0.737	>	0.176
Total TP	493	>	108
Total TN	383507	<	383563
Total FP	263	<	549
Total FP CONTRA	42	<	97
Total FP INCONS	134	<	408
Total FP COMP	87	>	44
Total FN	180	<	565
P-value	1.00475527001e-08

Comparison of performance of Multilign(seed) and Vsfold4. 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 Vsfold4).
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 Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(seed) and Vsfold4. 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 Vsfold4).

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	0.167
Average MCC ± 95% Confidence Intervals	0.153 ± 0.061
Sensitivity	0.160
Positive Predictive Value	0.176
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00619	-	0.16	0.18	0.14	7	22741	48	11	32	5	32
RFA_00626	rne5 links to Rfam database...	0.20	0.18	0.22	16	56543	61	11	46	4	71
RFA_00628	rne5 links to Rfam database...	0.24	0.22	0.26	19	57218	64	8	46	10	67
RFA_00630	rne5 links to Rfam database...	0.30	0.29	0.32	25	56875	58	3	50	5	62
RFA_00816	R2_retro_el links to Rfam database...	0.12	0.12	0.13	5	23181	42	9	25	8	36
RFA_00817	R2_retro_el links to Rfam database...	0.11	0.12	0.11	5	21898	42	16	26	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	20265	46	10	26	10	41
SRP_00241	Plant_SRP links to Rfam database...	0.07	0.07	0.08	6	45978	74	13	59	2	76
SRP_00331	Metazoa_SRP links to Rfam database...	0.14	0.13	0.16	11	37608	56	5	51	0	76
SRP_00340	Metazoa_SRP links to Rfam database...	0.18	0.17	0.19	14	41256	58	11	47	0	68

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