CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RNAshapes
MCC	0.720	>	0.498
Average MCC ± 95% Confidence Intervals	0.729 ± 0.164	>	0.460 ± 0.171
Sensitivity	0.722	>	0.526
Positive Predictive Value	0.719	>	0.475
Total TP	423	>	308
Total TN	326635	>	326574
Total FP	234	<	401
Total FP CONTRA	42	<	91
Total FP INCONS	123	<	250
Total FP COMP	69	>	60
Total FN	163	<	278
P-value	0.0

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

Total Scores
MCC	0.720
Average MCC ± 95% Confidence Intervals	0.729 ± 0.164
Sensitivity	0.722
Positive Predictive Value	0.719
Nr of predictions	9

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_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	0.498
Average MCC ± 95% Confidence Intervals	0.460 ± 0.171
Sensitivity	0.526
Positive Predictive Value	0.475
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00619	-	0.32	0.36	0.29	14	22742	45	9	26	10	25
RFA_00626	rne5 links to Rfam database...	0.45	0.45	0.46	39	56531	61	9	37	15	48
RFA_00628	rne5 links to Rfam database...	0.82	0.80	0.84	69	57209	33	1	12	20	17
RFA_00816	R2_retro_el links to Rfam database...	0.21	0.24	0.18	10	23164	47	18	28	1	31
RFA_00817	R2_retro_el links to Rfam database...	0.10	0.12	0.08	5	21881	60	21	38	1	36
RFA_00818	R2_retro_el links to Rfam database...	0.52	0.56	0.48	23	20253	31	9	16	6	18
SRP_00241	Plant_SRP links to Rfam database...	0.55	0.59	0.52	48	45963	47	13	32	2	34
SRP_00331	Metazoa_SRP links to Rfam database...	0.63	0.61	0.66	53	37595	30	2	25	3	34
SRP_00340	Metazoa_SRP links to Rfam database...	0.54	0.57	0.51	47	41236	47	9	36	2	35

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