CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Vsfold4		Carnac(seed)
MCC	0.317	>	0.161
Average MCC ± 95% Confidence Intervals	0.324 ± 0.054	>	0.119 ± 0.078
Sensitivity	0.292	>	0.027
Positive Predictive Value	0.347	<	0.962
Total TP	1095	>	101
Total TN	2088027	<	2091082
Total FP	2179	>	5
Total FP CONTRA	257	>	3
Total FP INCONS	1808	>	1
Total FP COMP	114	>	1
Total FN	2661	<	3655
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Vsfold4 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	1095
Total TN	2088027
Total FP	2179
Total FP CONTRA	257
Total FP INCONS	1808
Total FP COMP	114
Total FN	2661

Total Scores
MCC	0.317
Average MCC ± 95% Confidence Intervals	0.324 ± 0.054
Sensitivity	0.292
Positive Predictive Value	0.347
Nr of predictions	50

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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
ASE_00001	RNaseP_arch links to Rfam database...	0.52	0.45	0.60	34	34134	27	5	18	4	41
ASE_00002	RNaseP_arch links to Rfam database...	0.33	0.30	0.37	22	35451	38	2	36	0	51
ASE_00009	RNaseP_arch links to Rfam database...	0.20	0.18	0.22	12	26051	43	3	40	0	55
ASE_00014	RNaseP_arch links to Rfam database...	0.38	0.36	0.41	38	54192	56	7	48	1	68
ASE_00116	RNaseP_arch links to Rfam database...	0.17	0.15	0.19	10	31573	43	2	41	0	56
ASE_00120	RNaseP_arch links to Rfam database...	0.35	0.31	0.39	29	46897	45	3	42	0	65
ASE_00121	RNaseP_arch links to Rfam database...	0.20	0.17	0.22	16	45078	58	4	52	2	76
ASE_00145	RNaseP_arch links to Rfam database...	0.25	0.23	0.27	25	70033	69	3	64	2	86
ASE_00154	RNaseP_arch links to Rfam database...	0.34	0.30	0.40	32	65260	50	5	44	1	75
ASE_00155	RNaseP_arch links to Rfam database...	0.31	0.27	0.36	39	93419	73	2	68	3	103
ASE_00187	RNaseP_arch links to Rfam database...	0.25	0.23	0.28	26	68543	67	7	59	1	89
ASE_00196	RNaseP_arch links to Rfam database...	0.17	0.15	0.19	11	31569	47	4	42	1	64
ASE_00205	RNaseP_arch links to Rfam database...	0.19	0.18	0.20	16	45976	65	6	58	1	74
ASE_00209	RNaseP_arch links to Rfam database...	0.29	0.25	0.33	22	43004	45	2	43	0	66
ASE_00210	RNaseP_arch links to Rfam database...	0.10	0.09	0.11	6	27207	50	7	41	2	59
ASE_00213	RNaseP_arch links to Rfam database...	0.32	0.30	0.34	20	27203	40	10	28	2	46
ASE_00346	RNaseP_arch links to Rfam database...	0.23	0.21	0.26	20	48128	58	3	54	1	77
ASE_00359	RNaseP_arch links to Rfam database...	0.36	0.34	0.39	27	42708	43	4	39	0	53
ASE_00360	RNaseP_arch links to Rfam database...	0.20	0.20	0.21	13	29342	50	10	38	2	52
ASE_00417	RNaseP_arch links to Rfam database...	0.46	0.44	0.47	44	54522	50	3	46	1	56
ASE_00418	RNaseP_arch links to Rfam database...	0.29	0.27	0.32	20	38719	44	0	42	2	55
CRW_00016	Intron_gpI links to Rfam database...	0.53	0.46	0.61	55	77331	44	4	31	9	65
CRW_00610	Intron_gpI links to Rfam database...	0.40	0.36	0.46	29	36252	37	5	29	3	52
CRW_00613	Intron_gpI links to Rfam database...	0.48	0.42	0.54	33	34919	34	2	26	6	45
CRW_00618	Intron_gpI links to Rfam database...	0.33	0.31	0.35	19	56225	57	6	30	21	42
CRW_00633	Intron_gpI links to Rfam database...	0.38	0.35	0.42	37	63457	52	6	46	0	69
CRW_00634	Intron_gpI links to Rfam database...	0.29	0.28	0.30	26	64533	68	8	53	7	68
CRW_00670	Intron_gpI links to Rfam database...	0.37	0.34	0.41	41	70025	60	3	56	1	79
CRW_00671	Intron_gpI links to Rfam database...	0.55	0.50	0.60	59	62736	40	2	38	0	58
CRW_00672	Intron_gpI links to Rfam database...	0.30	0.29	0.32	32	72291	71	14	53	4	79
CRW_00674	Intron_gpI links to Rfam database...	0.29	0.26	0.33	32	83339	67	8	57	2	92
CRW_00676	Intron_gpI links to Rfam database...	0.34	0.34	0.34	39	93413	80	20	56	4	76
CRW_00692	Intron_gpI links to Rfam database...	0.26	0.24	0.28	22	68555	62	20	38	4	68
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.84	0.71	1.00	10	936	0	0	0	0	4
PDB_00716	HDV_ribozyme links to Rfam database...	0.17	0.17	0.18	4	2679	19	0	18	1	19
PDB_00827	Intron_gpI links to Rfam database...	0.65	0.54	0.79	44	26972	13	0	12	1	37
PDB_01092	glmS links to Rfam database...	0.66	0.58	0.77	30	10114	10	2	7	1	22
RFA_00597	Telomerase-vert links to Rfam database...	0.15	0.15	0.15	16	97796	96	11	80	5	93
RFA_00598	Telomerase-vert links to Rfam database...	0.14	0.13	0.14	13	84576	88	14	63	11	88
RFA_00601	Telomerase-vert links to Rfam database...	0.10	0.11	0.11	12	99122	105	21	80	4	102
RFA_00632	HDV_ribozyme links to Rfam database...	0.36	0.36	0.37	10	4068	17	3	14	0	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.58	0.57	0.59	16	3978	11	1	10	0	12
RFA_00767	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1878	13	1	12	0	18
RFA_00768	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1875	16	1	15	0	18
RFA_00769	Corona_pk3 links to Rfam database...	0.50	0.50	0.50	9	1935	9	4	5	0	9
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	2003	15	2	11	2	18
RFA_00773	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1936	19	1	16	2	18
RFA_00779	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	2	1	0	8
RFA_00808	RydC links to Rfam database...	0.62	0.56	0.69	9	2003	4	3	1	0	7
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	1	7	0	10

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

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

Total Base Pair Counts
Total TP	101
Total TN	2091082
Total FP	5
Total FP CONTRA	3
Total FP INCONS	1
Total FP COMP	1
Total FN	3655

Total Scores
MCC	0.161
Average MCC ± 95% Confidence Intervals	0.119 ± 0.078
Sensitivity	0.027
Positive Predictive Value	0.962
Nr of predictions	50

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00001	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	34191	0	0	0	0	75
ASE_00002	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	35511	0	0	0	0	73
ASE_00009	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	26106	0	0	0	0	67
ASE_00014	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	54285	0	0	0	0	106
ASE_00116	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	31626	0	0	0	0	66
ASE_00120	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	46971	0	0	0	0	94
ASE_00121	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	45150	0	0	0	0	92
ASE_00145	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	70125	0	0	0	0	111
ASE_00154	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	65341	0	0	0	0	107
ASE_00155	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	93528	0	0	0	0	142
ASE_00187	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	68635	0	0	0	0	115
ASE_00196	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	31626	0	0	0	0	75
ASE_00205	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	90
ASE_00209	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	43071	0	0	0	0	88
ASE_00210	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	27261	0	0	0	0	65
ASE_00213	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	27261	0	0	0	0	66
ASE_00346	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	48205	0	0	0	0	97
ASE_00359	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	42778	0	0	0	0	80
ASE_00360	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	29403	0	0	0	0	65
ASE_00417	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	54615	0	0	0	0	100
ASE_00418	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	38781	0	0	0	0	75
CRW_00016	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	77421	0	0	0	0	120
CRW_00610	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	36315	0	0	0	0	81
CRW_00613	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	34980	0	0	0	0	78
CRW_00618	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	56280	0	0	0	0	61
CRW_00633	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	63546	0	0	0	0	106
CRW_00634	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	64620	0	0	0	0	94
CRW_00670	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	70125	0	0	0	0	120
CRW_00671	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	62835	0	0	0	0	117
CRW_00672	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	72390	0	0	0	0	111
CRW_00674	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	83436	0	0	0	0	124
CRW_00676	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	93528	0	0	0	0	115
CRW_00692	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	68635	0	0	0	0	90
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00716	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	23
PDB_00827	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	27028	0	0	0	0	81
PDB_01092	glmS links to Rfam database...	0.77	0.63	0.94	33	10118	3	1	1	1	19
RFA_00597	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	97903	0	0	0	0	109
RFA_00598	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	84666	0	0	0	0	101
RFA_00601	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	99235	0	0	0	0	114
RFA_00632	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	4095	0	0	0	0	28
RFA_00636	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	4005	0	0	0	0	28
RFA_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	1	1	0	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.62	0.39	1.00	7	2009	0	0	0	0	11
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	1	1	0	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1943	0	0	0	0	8
RFA_00808	RydC links to Rfam database...	0.00	0.00	0.00	0	2016	0	0	0	0	16
RFA_00809	RydC links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	16

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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 Vsfold4 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold4

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

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

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

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