CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PPfold(seed)		Vsfold5
MCC	0.735	>	0.192
Average MCC ± 95% Confidence Intervals	0.762 ± 0.075	>	0.197 ± 0.047
Sensitivity	0.691	>	0.185
Positive Predictive Value	0.783	>	0.201
Total TP	1194	>	320
Total TN	916973	>	916908
Total FP	467	<	1355
Total FP CONTRA	48	<	206
Total FP INCONS	283	<	1064
Total FP COMP	136	>	85
Total FN	535	<	1409
P-value	5.23657817852e-08

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Performance plots

Comparison of performance of PPfold(seed) and Vsfold5. 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 PPfold(seed) and Vsfold5).
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 PPfold(seed) and Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(seed) and Vsfold5. 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 PPfold(seed) and Vsfold5).

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Performance of PPfold(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PPfold(seed)

Total Base Pair Counts
Total TP	1194
Total TN	916973
Total FP	467
Total FP CONTRA	48
Total FP INCONS	283
Total FP COMP	136
Total FN	535

Total Scores
MCC	0.735
Average MCC ± 95% Confidence Intervals	0.762 ± 0.075
Sensitivity	0.691
Positive Predictive Value	0.783
Nr of predictions	22

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2. Individual counts for PPfold(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00626	rne5 links to Rfam database...	0.94	0.89	1.00	77	56539	1	0	0	1	10
RFA_00627	rne5 links to Rfam database...	0.95	0.91	1.00	79	56874	4	0	0	4	8
RFA_00628	rne5 links to Rfam database...	0.95	0.91	1.00	78	57213	2	0	0	2	8
RFA_00630	rne5 links to Rfam database...	0.91	0.85	0.97	74	56877	5	0	2	3	13
RFA_00814	R2_retro_el links to Rfam database...	0.94	0.88	1.00	36	25164	2	0	0	2	5
RFA_00816	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	23183	2	0	0	2	4
RFA_00817	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	21908	1	0	0	1	4
RFA_00818	R2_retro_el links to Rfam database...	0.94	0.88	1.00	36	20265	2	0	0	2	5
RFA_00819	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	27929	2	0	0	2	4
SRP_00079	Plant_SRP links to Rfam database...	0.74	0.69	0.79	61	41828	28	0	16	12	27
SRP_00099	Plant_SRP links to Rfam database...	0.60	0.59	0.62	56	44760	40	2	32	6	39
SRP_00124	Metazoa_SRP links to Rfam database...	0.71	0.66	0.76	56	37054	27	3	15	9	29
SRP_00182	Plant_SRP links to Rfam database...	0.85	0.78	0.92	79	45970	17	0	7	10	22
SRP_00241	Plant_SRP links to Rfam database...	0.53	0.52	0.54	43	45977	49	9	27	13	39
SRP_00252	Metazoa_SRP links to Rfam database...	0.64	0.63	0.64	56	49054	42	5	26	11	33
SRP_00253	Metazoa_SRP links to Rfam database...	0.64	0.62	0.66	56	49370	40	5	24	11	34
SRP_00257	Metazoa_SRP links to Rfam database...	0.51	0.44	0.59	48	50959	36	5	28	3	60
SRP_00260	Metazoa_SRP links to Rfam database...	0.56	0.51	0.61	51	47811	39	5	28	6	49
SRP_00328	Metazoa_SRP links to Rfam database...	0.61	0.56	0.67	48	39549	29	5	19	5	37
SRP_00329	Metazoa_SRP links to Rfam database...	0.72	0.67	0.78	57	39830	26	2	14	10	28
SRP_00331	Metazoa_SRP links to Rfam database...	0.63	0.59	0.69	51	37601	31	2	21	8	36
SRP_00340	Metazoa_SRP links to Rfam database...	0.54	0.50	0.59	41	41258	42	5	24	13	41

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Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	320
Total TN	916908
Total FP	1355
Total FP CONTRA	206
Total FP INCONS	1064
Total FP COMP	85
Total FN	1409

Total Scores
MCC	0.192
Average MCC ± 95% Confidence Intervals	0.197 ± 0.047
Sensitivity	0.185
Positive Predictive Value	0.201
Nr of predictions	22

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2. Individual counts for Vsfold5 [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00626	rne5 links to Rfam database...	0.31	0.31	0.32	27	56531	62	15	43	4	60
RFA_00627	rne5 links to Rfam database...	0.26	0.26	0.26	23	56863	69	16	51	2	64
RFA_00628	rne5 links to Rfam database...	0.34	0.35	0.34	30	57202	66	13	46	7	56
RFA_00630	rne5 links to Rfam database...	0.27	0.29	0.26	25	56857	78	13	58	7	62
RFA_00814	R2_retro_el links to Rfam database...	0.31	0.34	0.29	14	25151	46	10	25	11	27
RFA_00816	R2_retro_el links to Rfam database...	0.31	0.32	0.30	13	23177	38	12	18	8	28
RFA_00817	R2_retro_el links to Rfam database...	0.32	0.34	0.30	14	21898	35	10	23	2	27
RFA_00818	R2_retro_el links to Rfam database...	0.19	0.20	0.19	8	20258	41	8	27	6	33
RFA_00819	R2_retro_el links to Rfam database...	0.27	0.27	0.28	11	27926	53	6	23	24	30
SRP_00079	Plant_SRP links to Rfam database...	0.14	0.14	0.15	12	41823	72	4	66	2	76
SRP_00099	Plant_SRP links to Rfam database...	0.07	0.06	0.08	6	44770	74	8	66	0	89
SRP_00124	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	37128	0	0	0	0	85
SRP_00182	Plant_SRP links to Rfam database...	0.16	0.16	0.17	16	45964	76	7	69	0	85
SRP_00241	Plant_SRP links to Rfam database...	0.07	0.07	0.07	6	45966	85	13	71	1	76
SRP_00252	Metazoa_SRP links to Rfam database...	0.18	0.18	0.17	16	49049	79	7	69	3	73
SRP_00253	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	49361	96	14	80	2	90
SRP_00257	Metazoa_SRP links to Rfam database...	0.30	0.27	0.34	29	50955	58	2	54	2	79
SRP_00260	Metazoa_SRP links to Rfam database...	0.12	0.11	0.13	11	47812	72	7	65	0	89
SRP_00328	Metazoa_SRP links to Rfam database...	0.19	0.18	0.21	15	39548	60	10	48	2	70
SRP_00329	Metazoa_SRP links to Rfam database...	0.23	0.22	0.25	19	39826	58	15	43	0	66
SRP_00331	Metazoa_SRP links to Rfam database...	0.19	0.18	0.21	16	37597	62	7	55	0	71
SRP_00340	Metazoa_SRP links to Rfam database...	0.11	0.11	0.11	9	41246	75	9	64	2	73

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

Table of contents:

Overview

Performance plots

Performance of PPfold(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PPfold(seed)

2. Individual counts for PPfold(seed) [ download as .csv ]

Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ download as .csv ]