CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		PETfold_pre2.0(seed)
MCC	0.789	>	0.764
Average MCC ± 95% Confidence Intervals	0.808 ± 0.070	>	0.801 ± 0.096
Sensitivity	0.762	>	0.719
Positive Predictive Value	0.818	>	0.813
Total TP	987	>	932
Total TN	761508	<	761569
Total FP	363	>	355
Total FP CONTRA	38	>	31
Total FP INCONS	182	<	183
Total FP COMP	143	>	141
Total FN	309	<	364
P-value	3.73923511064e-08

Comparison of performance of TurboFold(seed) and PETfold_pre2.0(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 TurboFold(seed) and PETfold_pre2.0(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 TurboFold(seed) and PETfold_pre2.0(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(seed) and PETfold_pre2.0(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 TurboFold(seed) and PETfold_pre2.0(seed)).

Total Scores
MCC	0.789
Average MCC ± 95% Confidence Intervals	0.808 ± 0.070
Sensitivity	0.762
Positive Predictive Value	0.818
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00210	RNaseP_arch links to Rfam database...	0.71	0.68	0.75	44	27202	16	4	11	1	21
RFA_00626	rne5 links to Rfam database...	0.90	0.85	0.95	74	56538	17	0	4	13	13
RFA_00627	rne5 links to Rfam database...	0.85	0.82	0.89	71	56873	23	0	9	14	16
RFA_00628	rne5 links to Rfam database...	0.92	0.90	0.95	77	57210	17	0	4	13	9
RFA_00630	rne5 links to Rfam database...	0.83	0.79	0.87	69	56874	22	0	10	12	18
RFA_00805	RNAIII links to Rfam database...	0.87	0.82	0.93	123	133254	13	0	9	4	27
RFA_00814	R2_retro_el links to Rfam database...	0.92	0.85	1.00	35	25165	13	0	0	13	6
RFA_00816	R2_retro_el links to Rfam database...	1.00	1.00	1.00	41	23179	14	0	0	14	0
RFA_00817	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	21908	7	0	0	7	4
RFA_00818	R2_retro_el links to Rfam database...	0.85	0.80	0.89	33	20264	11	1	3	7	8
RFA_00819	R2_retro_el links to Rfam database...	0.98	0.95	1.00	39	27927	27	0	0	27	2
SRP_00241	Plant_SRP links to Rfam database...	0.56	0.59	0.54	48	45967	43	12	29	2	34
SRP_00257	Metazoa_SRP links to Rfam database...	0.78	0.72	0.85	78	50948	16	4	10	2	30
SRP_00328	Metazoa_SRP links to Rfam database...	0.69	0.67	0.70	57	39540	27	5	19	3	28
SRP_00329	Metazoa_SRP links to Rfam database...	0.65	0.64	0.67	54	39822	30	3	24	3	31
SRP_00331	Metazoa_SRP links to Rfam database...	0.67	0.66	0.68	57	37591	29	3	24	2	30
SRP_00340	Metazoa_SRP links to Rfam database...	0.61	0.61	0.61	50	41246	38	6	26	6	32

Total Scores
MCC	0.764
Average MCC ± 95% Confidence Intervals	0.801 ± 0.096
Sensitivity	0.719
Positive Predictive Value	0.813
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00210	RNaseP_arch links to Rfam database...	0.68	0.65	0.71	42	27202	24	2	15	7	23
RFA_00626	rne5 links to Rfam database...	0.96	0.92	1.00	80	56536	7	0	0	7	7
RFA_00627	rne5 links to Rfam database...	0.96	0.93	1.00	81	56872	12	0	0	12	6
RFA_00628	rne5 links to Rfam database...	0.96	0.93	1.00	80	57211	12	0	0	12	6
RFA_00630	rne5 links to Rfam database...	0.92	0.87	0.97	76	56875	17	0	2	15	11
RFA_00805	RNAIII links to Rfam database...	0.64	0.49	0.84	73	133299	16	0	14	2	77
RFA_00814	R2_retro_el links to Rfam database...	0.98	0.95	1.00	39	25161	5	0	0	5	2
RFA_00816	R2_retro_el links to Rfam database...	0.98	0.95	1.00	39	23181	6	0	0	6	2
RFA_00817	R2_retro_el links to Rfam database...	0.98	0.95	1.00	39	21906	4	0	0	4	2
RFA_00818	R2_retro_el links to Rfam database...	0.98	0.95	1.00	39	20262	3	0	0	3	2
RFA_00819	R2_retro_el links to Rfam database...	0.98	0.95	1.00	39	27927	6	0	0	6	2
SRP_00241	Plant_SRP links to Rfam database...	0.55	0.56	0.55	46	45972	53	9	29	15	36
SRP_00257	Metazoa_SRP links to Rfam database...	0.53	0.48	0.58	52	50950	42	5	33	4	56
SRP_00328	Metazoa_SRP links to Rfam database...	0.61	0.59	0.64	50	39543	34	5	23	6	35
SRP_00329	Metazoa_SRP links to Rfam database...	0.75	0.72	0.78	61	39825	29	2	15	12	24
SRP_00331	Metazoa_SRP links to Rfam database...	0.65	0.61	0.69	53	37598	34	2	22	10	34
SRP_00340	Metazoa_SRP links to Rfam database...	0.53	0.52	0.54	43	41249	51	6	30	15	39

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