CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		RSpredict(seed)
MCC	0.787	>	0.016
Average MCC ± 95% Confidence Intervals	0.805 ± 0.066	>	0.011 ± 0.014
Sensitivity	0.760	>	0.015
Positive Predictive Value	0.815	>	0.019
Total TP	1052	>	21
Total TN	797739	<	797932
Total FP	383	<	1113
Total FP CONTRA	40	<	186
Total FP INCONS	199	<	891
Total FP COMP	144	>	36
Total FN	332	<	1363
P-value	3.30280588002e-08

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

Total Scores
MCC	0.787
Average MCC ± 95% Confidence Intervals	0.805 ± 0.066
Sensitivity	0.760
Positive Predictive Value	0.815
Nr of predictions	18

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_00308	Bacteria_large_SRP links to Rfam database...	0.76	0.74	0.77	65	36231	20	2	17	1	23
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	0.016
Average MCC ± 95% Confidence Intervals	0.011 ± 0.014
Sensitivity	0.015
Positive Predictive Value	0.019
Nr of predictions	18

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...	0.00	0.00	0.00	0	27244	17	5	12	0	65
RFA_00626	rne5 links to Rfam database...	0.00	0.00	0.00	0	56534	83	16	66	1	87
RFA_00627	rne5 links to Rfam database...	0.00	0.00	0.00	0	56869	84	21	63	0	87
RFA_00628	rne5 links to Rfam database...	0.00	0.00	0.00	0	57206	85	25	60	0	86
RFA_00630	rne5 links to Rfam database...	0.07	0.07	0.07	6	56872	79	18	57	4	81
RFA_00805	RNAIII links to Rfam database...	0.07	0.06	0.08	9	133271	106	9	97	0	141
RFA_00814	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	25168	36	2	30	4	41
RFA_00816	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	23193	37	5	22	10	41
RFA_00817	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	21919	34	5	21	8	41
RFA_00818	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	20276	28	2	23	3	41
RFA_00819	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	27928	44	7	31	6	41
SRP_00241	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	45983	73	13	60	0	82
SRP_00257	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	50958	82	6	76	0	108
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.08	0.07	0.09	6	36247	62	14	48	0	82
SRP_00328	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	39557	64	8	56	0	85
SRP_00329	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	39842	61	8	53	0	85
SRP_00331	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	37606	69	9	60	0	87
SRP_00340	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	41259	69	13	56	0	82

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