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)		CentroidFold
MCC	0.716	>	0.655
Average MCC ± 95% Confidence Intervals	0.749 ± 0.077	>	0.639 ± 0.076
Sensitivity	0.652	>	0.634
Positive Predictive Value	0.787	>	0.679
Total TP	1226	>	1191
Total TN	1050327	>	1050129
Total FP	467	<	705
Total FP CONTRA	48	<	116
Total FP INCONS	283	<	448
Total FP COMP	136	<	141
Total FN	653	<	688
P-value	5.19332990918e-08

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Performance plots

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

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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	1226
Total TN	1050327
Total FP	467
Total FP CONTRA	48
Total FP INCONS	283
Total FP COMP	136
Total FN	653

Total Scores
MCC	0.716
Average MCC ± 95% Confidence Intervals	0.749 ± 0.077
Sensitivity	0.652
Positive Predictive Value	0.787
Nr of predictions	23

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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_00805	RNAIII links to Rfam database...	0.46	0.21	1.00	32	133354	0	0	0	0	118
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 CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	1191
Total TN	1050129
Total FP	705
Total FP CONTRA	116
Total FP INCONS	448
Total FP COMP	141
Total FN	688

Total Scores
MCC	0.655
Average MCC ± 95% Confidence Intervals	0.639 ± 0.076
Sensitivity	0.634
Positive Predictive Value	0.679
Nr of predictions	23

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2. Individual counts for CentroidFold [ 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...	0.90	0.86	0.95	75	56537	20	0	4	16	12
RFA_00627	rne5 links to Rfam database...	0.87	0.82	0.93	71	56877	18	0	5	13	16
RFA_00628	rne5 links to Rfam database...	0.90	0.86	0.94	74	57212	20	0	5	15	12
RFA_00630	rne5 links to Rfam database...	0.80	0.76	0.85	66	56875	25	0	12	13	21
RFA_00805	RNAIII links to Rfam database...	0.80	0.64	1.00	96	133290	0	0	0	0	54
RFA_00814	R2_retro_el links to Rfam database...	0.70	0.51	0.95	21	25178	6	0	1	5	20
RFA_00816	R2_retro_el links to Rfam database...	0.75	0.73	0.77	30	23181	14	8	1	5	11
RFA_00817	R2_retro_el links to Rfam database...	0.13	0.12	0.14	5	21909	31	9	22	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.54	0.54	0.54	22	20260	26	11	8	7	19
RFA_00819	R2_retro_el links to Rfam database...	0.49	0.37	0.65	15	27943	23	0	8	15	26
SRP_00079	Plant_SRP links to Rfam database...	0.63	0.61	0.64	54	41821	39	3	27	9	34
SRP_00099	Plant_SRP links to Rfam database...	0.62	0.62	0.63	59	44756	36	6	29	1	36
SRP_00124	Metazoa_SRP links to Rfam database...	0.63	0.60	0.66	51	37051	32	1	25	6	34
SRP_00182	Plant_SRP links to Rfam database...	0.58	0.56	0.61	57	45962	40	10	27	3	44
SRP_00241	Plant_SRP links to Rfam database...	0.52	0.55	0.49	45	45964	49	14	33	2	37
SRP_00252	Metazoa_SRP links to Rfam database...	0.54	0.56	0.53	50	49046	50	6	39	5	39
SRP_00253	Metazoa_SRP links to Rfam database...	0.47	0.48	0.47	43	49364	53	9	39	5	47
SRP_00257	Metazoa_SRP links to Rfam database...	0.85	0.82	0.87	89	50938	18	0	13	5	19
SRP_00260	Metazoa_SRP links to Rfam database...	0.71	0.73	0.70	73	47790	35	5	27	3	27
SRP_00328	Metazoa_SRP links to Rfam database...	0.60	0.61	0.58	52	39532	40	10	27	3	33
SRP_00329	Metazoa_SRP links to Rfam database...	0.62	0.61	0.63	52	39821	35	5	25	5	33
SRP_00331	Metazoa_SRP links to Rfam database...	0.53	0.53	0.53	46	37589	43	8	32	3	41
SRP_00340	Metazoa_SRP links to Rfam database...	0.51	0.55	0.47	45	41233	52	11	39	2	37

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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 CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

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