CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PETfold_pre2.0(seed)		PPfold(seed)
MCC	0.740	>	0.716
Average MCC ± 95% Confidence Intervals	0.773 ± 0.076	>	0.749 ± 0.077
Sensitivity	0.706	>	0.652
Positive Predictive Value	0.776	<	0.787
Total TP	1327	>	1226
Total TN	1050175	<	1050327
Total FP	589	>	467
Total FP CONTRA	52	>	48
Total FP INCONS	330	>	283
Total FP COMP	207	>	136
Total FN	552	<	653
P-value	5.10776592382e-08

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Performance plots

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

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Performance of PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

Total Base Pair Counts
Total TP	1327
Total TN	1050175
Total FP	589
Total FP CONTRA	52
Total FP INCONS	330
Total FP COMP	207
Total FN	552

Total Scores
MCC	0.740
Average MCC ± 95% Confidence Intervals	0.773 ± 0.076
Sensitivity	0.706
Positive Predictive Value	0.776
Nr of predictions	23

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2. Individual counts for PETfold_pre2.0(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...	0.96	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_00079	Plant_SRP links to Rfam database...	0.76	0.73	0.80	64	41825	30	0	16	14	24
SRP_00099	Plant_SRP links to Rfam database...	0.62	0.62	0.63	59	44756	41	3	32	6	36
SRP_00124	Metazoa_SRP links to Rfam database...	0.71	0.68	0.74	58	37050	32	3	17	12	27
SRP_00182	Plant_SRP links to Rfam database...	0.88	0.84	0.91	85	45963	17	0	8	9	16
SRP_00241	Plant_SRP links to Rfam database...	0.55	0.56	0.55	46	45972	53	9	29	15	36
SRP_00252	Metazoa_SRP links to Rfam database...	0.64	0.66	0.63	59	49047	47	6	29	12	30
SRP_00253	Metazoa_SRP links to Rfam database...	0.65	0.66	0.64	59	49363	45	5	28	12	31
SRP_00257	Metazoa_SRP links to Rfam database...	0.53	0.48	0.58	52	50950	42	5	33	4	56
SRP_00260	Metazoa_SRP links to Rfam database...	0.55	0.53	0.58	53	47804	46	6	32	8	47
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

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Performance of PPfold(seed) - scored lower 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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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 PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

2. Individual counts for PETfold_pre2.0(seed) [ download as .csv ]

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

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

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