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)		Vsfold4
MCC	0.735	>	0.197
Average MCC ± 95% Confidence Intervals	0.762 ± 0.075	>	0.192 ± 0.046
Sensitivity	0.691	>	0.182
Positive Predictive Value	0.783	>	0.215
Total TP	1194	>	315
Total TN	916973	<	917033
Total FP	467	<	1225
Total FP CONTRA	48	<	173
Total FP INCONS	283	<	977
Total FP COMP	136	>	75
Total FN	535	<	1414
P-value	5.06544643719e-08

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Performance plots

Comparison of performance of PPfold(seed) and Vsfold4. 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 Vsfold4).
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 Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(seed) and Vsfold4. 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 Vsfold4).

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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 Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	315
Total TN	917033
Total FP	1225
Total FP CONTRA	173
Total FP INCONS	977
Total FP COMP	75
Total FN	1414

Total Scores
MCC	0.197
Average MCC ± 95% Confidence Intervals	0.192 ± 0.046
Sensitivity	0.182
Positive Predictive Value	0.215
Nr of predictions	22

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2. Individual counts for Vsfold4 [ 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...	0.20	0.18	0.22	16	56543	61	11	46	4	71
RFA_00627	rne5 links to Rfam database...	0.23	0.22	0.24	19	56874	63	13	47	3	68
RFA_00628	rne5 links to Rfam database...	0.24	0.22	0.26	19	57218	64	8	46	10	67
RFA_00630	rne5 links to Rfam database...	0.30	0.29	0.32	25	56875	58	3	50	5	62
RFA_00814	R2_retro_el links to Rfam database...	0.41	0.39	0.43	16	25163	33	3	18	12	25
RFA_00816	R2_retro_el links to Rfam database...	0.12	0.12	0.13	5	23181	42	9	25	8	36
RFA_00817	R2_retro_el links to Rfam database...	0.11	0.12	0.11	5	21898	42	16	26	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	20265	46	10	26	10	41
RFA_00819	R2_retro_el links to Rfam database...	0.20	0.20	0.21	8	27928	45	6	24	15	33
SRP_00079	Plant_SRP links to Rfam database...	0.09	0.09	0.10	8	41827	71	4	66	1	80
SRP_00099	Plant_SRP links to Rfam database...	0.27	0.24	0.31	23	44776	51	7	44	0	72
SRP_00124	Metazoa_SRP links to Rfam database...	0.16	0.14	0.19	12	37066	50	5	45	0	73
SRP_00182	Plant_SRP links to Rfam database...	0.34	0.32	0.36	32	45968	56	10	46	0	69
SRP_00241	Plant_SRP links to Rfam database...	0.07	0.07	0.08	6	45978	74	13	59	2	76
SRP_00252	Metazoa_SRP links to Rfam database...	0.13	0.12	0.13	11	49058	75	11	61	3	78
SRP_00253	Metazoa_SRP links to Rfam database...	0.15	0.14	0.16	13	49376	68	7	59	2	77
SRP_00257	Metazoa_SRP links to Rfam database...	0.10	0.08	0.13	9	50971	60	1	59	0	99
SRP_00260	Metazoa_SRP links to Rfam database...	0.40	0.36	0.45	36	47815	44	4	40	0	64
SRP_00328	Metazoa_SRP links to Rfam database...	0.18	0.16	0.20	14	39550	57	11	46	0	71
SRP_00329	Metazoa_SRP links to Rfam database...	0.17	0.15	0.20	13	39839	51	5	46	0	72
SRP_00331	Metazoa_SRP links to Rfam database...	0.14	0.13	0.16	11	37608	56	5	51	0	76
SRP_00340	Metazoa_SRP links to Rfam database...	0.18	0.17	0.19	14	41256	58	11	47	0	68

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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 Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

2. Individual counts for Vsfold4 [ download as .csv ]