CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Carnac(seed)		Mastr(seed)
MCC	0.141	>	0.097
Average MCC ± 95% Confidence Intervals	0.097 ± 0.065	>	0.082 ± 0.055
Sensitivity	0.021	>	0.014
Positive Predictive Value	0.962	>	0.670
Total TP	101	>	69
Total TN	3463490	<	3463492
Total FP	5	<	37
Total FP CONTRA	3	<	5
Total FP INCONS	1	<	29
Total FP COMP	1	<	3
Total FN	4755	<	4787
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	101
Total TN	3463490
Total FP	5
Total FP CONTRA	3
Total FP INCONS	1
Total FP COMP	1
Total FN	4755

Total Scores
MCC	0.141
Average MCC ± 95% Confidence Intervals	0.097 ± 0.065
Sensitivity	0.021
Positive Predictive Value	0.962
Nr of predictions	61

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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_00148	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	112575	0	0	0	0	154
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_00222	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	112101	0	0	0	0	157
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_00013	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	103740	0	0	0	0	115
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_00614	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	121771	0	0	0	0	57
CRW_00618	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	56280	0	0	0	0	61
CRW_00619	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	165025	0	0	0	0	73
CRW_00620	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	150975	0	0	0	0	63
CRW_00621	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	153181	0	0	0	0	71
CRW_00623	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	129795	0	0	0	0	83
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_00599	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	101475	0	0	0	0	111
RFA_00600	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	120295	0	0	0	0	100
RFA_00601	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	99235	0	0	0	0	114
RFA_00602	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	101475	0	0	0	0	116
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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Performance of Mastr(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	69
Total TN	3463492
Total FP	37
Total FP CONTRA	5
Total FP INCONS	29
Total FP COMP	3
Total FN	4787

Total Scores
MCC	0.097
Average MCC ± 95% Confidence Intervals	0.082 ± 0.055
Sensitivity	0.014
Positive Predictive Value	0.670
Nr of predictions	61

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2. Individual counts for Mastr(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_00148	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	112575	0	0	0	0	154
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_00222	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	112101	0	0	0	0	157
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_00013	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	103740	0	0	0	0	115
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_00614	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	121771	0	0	0	0	57
CRW_00618	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	56280	0	0	0	0	61
CRW_00619	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	165025	0	0	0	0	73
CRW_00620	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	150975	0	0	0	0	63
CRW_00621	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	153181	0	0	0	0	71
CRW_00623	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	129795	0	0	0	0	83
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...	0.60	0.43	0.86	6	939	2	0	1	1	8
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...	0.00	0.00	0.00	0	10153	0	0	0	0	52
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_00599	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	101475	0	0	0	0	111
RFA_00600	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	120295	0	0	0	0	100
RFA_00601	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	99235	0	0	0	0	114
RFA_00602	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	101475	0	0	0	0	116
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...	0.67	0.50	0.90	9	1881	1	0	1	0	9
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...	0.64	0.50	0.82	9	1942	2	1	1	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	2	0	2	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.64	0.50	0.82	9	1942	2	1	1	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	0	3	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	17	2	13	2	16
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	1	7	0	10

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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 Carnac(seed) - scored higher in this pairwise comparison

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

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

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

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

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