CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNASampler(20)		RNAwolf
MCC	0.565	>	0.325
Average MCC ± 95% Confidence Intervals	0.539 ± 0.043	>	0.328 ± 0.039
Sensitivity	0.413	>	0.340
Positive Predictive Value	0.772	>	0.313
Total TP	3079	>	2536
Total TN	4282091	>	4277970
Total FP	1146	<	6280
Total FP CONTRA	258	<	1043
Total FP INCONS	649	<	4528
Total FP COMP	239	<	709
Total FN	4370	<	4913
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNASampler(20) and RNAwolf. 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 RNASampler(20) and RNAwolf).
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 RNASampler(20) and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(20) and RNAwolf. 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 RNASampler(20) and RNAwolf).

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Performance of RNASampler(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RNASampler(20)

Total Base Pair Counts
Total TP	3079
Total TN	4282091
Total FP	1146
Total FP CONTRA	258
Total FP INCONS	649
Total FP COMP	239
Total FN	4370

Total Scores
MCC	0.565
Average MCC ± 95% Confidence Intervals	0.539 ± 0.043
Sensitivity	0.413
Positive Predictive Value	0.772
Nr of predictions	78

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2. Individual counts for RNASampler(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00064	RNaseP_bact_a links to Rfam database...	0.44	0.34	0.58	30	45399	23	1	21	1	59
ASE_00090	RNaseP_bact_a links to Rfam database...	0.54	0.40	0.74	40	55557	14	0	14	0	61
ASE_00135	RNaseP_bact_a links to Rfam database...	0.54	0.36	0.83	39	63143	16	0	8	8	70
ASE_00153	RNaseP_nuc links to Rfam database...	0.38	0.33	0.44	24	57576	38	7	23	8	49
ASE_00215	RNaseP_bact_a links to Rfam database...	0.38	0.23	0.62	23	48479	16	0	14	2	76
ASE_00305	RNaseP_bact_b links to Rfam database...	0.78	0.71	0.86	60	54545	14	1	9	4	25
ASE_00328	RNaseP_bact_b links to Rfam database...	0.70	0.57	0.85	64	72696	14	5	6	3	48
ASE_00361	RNaseP_bact_a links to Rfam database...	0.34	0.21	0.55	27	75417	26	3	19	4	100
ASE_00427	RNaseP_nuc links to Rfam database...	0.57	0.46	0.72	21	40726	18	1	7	10	25
ASE_00441	RNaseP_bact_a links to Rfam database...	0.46	0.31	0.69	35	64210	16	0	16	0	77
SRP_00006	Metazoa_SRP links to Rfam database...	0.87	0.76	0.99	77	45675	4	0	1	3	24
SRP_00011	Plant_SRP links to Rfam database...	0.55	0.42	0.71	44	46298	18	4	14	0	60
SRP_00015	Plant_SRP links to Rfam database...	0.74	0.59	0.94	58	46298	5	3	1	1	41
SRP_00024	Bacteria_large_SRP links to Rfam database...	0.28	0.08	1.00	7	37668	0	0	0	0	80
SRP_00026	Bacteria_large_SRP links to Rfam database...	0.51	0.27	0.96	24	36831	1	0	1	0	64
SRP_00030	Bacteria_large_SRP links to Rfam database...	0.28	0.08	1.00	7	36849	0	0	0	0	81
SRP_00031	Bacteria_large_SRP links to Rfam database...	0.35	0.12	1.00	11	36304	0	0	0	0	78
SRP_00037	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	36585	0	0	0	0	87
SRP_00050	Metazoa_SRP links to Rfam database...	0.86	0.76	0.99	75	44774	3	0	1	2	24
SRP_00066	Metazoa_SRP links to Rfam database...	0.81	0.66	0.99	66	45384	1	0	1	0	34
SRP_00086	Metazoa_SRP links to Rfam database...	0.87	0.77	0.99	77	44175	3	0	1	2	23
SRP_00088	Bacteria_large_SRP links to Rfam database...	0.40	0.16	1.00	14	34177	0	0	0	0	75
SRP_00089	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	35778	0	0	0	0	90
SRP_00090	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	35511	0	0	0	0	90
SRP_00102	Metazoa_SRP links to Rfam database...	0.86	0.77	0.95	78	44469	4	0	4	0	23
SRP_00103	Metazoa_SRP links to Rfam database...	0.80	0.64	1.00	65	45386	0	0	0	0	37
SRP_00152	Plant_SRP links to Rfam database...	0.52	0.27	1.00	28	45725	0	0	0	0	75
SRP_00171	Metazoa_SRP links to Rfam database...	0.74	0.61	0.89	54	45390	7	2	5	0	34
SRP_00178	Plant_SRP links to Rfam database...	0.36	0.13	1.00	13	45740	0	0	0	0	89
SRP_00179	Plant_SRP links to Rfam database...	0.39	0.16	0.94	17	46038	1	0	1	0	88
SRP_00181	Plant_SRP links to Rfam database...	0.41	0.17	1.00	17	46039	0	0	0	0	85
SRP_00182	Plant_SRP links to Rfam database...	0.78	0.66	0.92	67	45983	6	0	6	0	34
SRP_00188	Plant_SRP links to Rfam database...	0.26	0.14	0.48	11	31102	12	1	11	0	68
SRP_00228	Metazoa_SRP links to Rfam database...	0.88	0.78	0.99	74	45376	7	0	1	6	21
SRP_00234	Bacteria_large_SRP links to Rfam database...	0.47	0.23	0.95	20	36294	1	0	1	0	66
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.28	0.08	1.00	7	36308	0	0	0	0	81
SRP_00317	Metazoa_SRP links to Rfam database...	0.76	0.61	0.95	60	45087	8	0	3	5	38
SRP_00335	Bacteria_large_SRP links to Rfam database...	0.42	0.18	1.00	7	35238	0	0	0	0	32
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.38	0.14	1.00	13	35498	0	0	0	0	78
SRP_00347	Metazoa_SRP links to Rfam database...	0.80	0.66	0.98	63	46601	5	0	1	4	33
SRP_00368	Metazoa_SRP links to Rfam database...	0.77	0.59	1.00	58	43898	2	0	0	2	40
TMR_00017	tmRNA links to Rfam database...	0.60	0.45	0.81	46	67104	15	2	9	4	56
TMR_00018	tmRNA links to Rfam database...	0.52	0.41	0.64	38	64561	25	10	11	4	54
TMR_00042	tmRNA links to Rfam database...	0.60	0.42	0.85	41	62787	13	0	7	6	57
TMR_00046	tmRNA links to Rfam database...	0.48	0.40	0.58	38	62769	34	5	23	6	58
TMR_00048	tmRNA links to Rfam database...	0.61	0.46	0.80	44	64925	16	3	8	5	51
TMR_00080	tmRNA links to Rfam database...	0.49	0.41	0.60	39	70435	28	10	16	2	57
TMR_00082	tmRNA links to Rfam database...	0.43	0.31	0.59	30	67845	21	13	8	0	66
TMR_00123	tmRNA links to Rfam database...	0.60	0.46	0.79	46	66372	17	3	9	5	55
TMR_00137	tmRNA links to Rfam database...	0.47	0.37	0.59	33	61019	28	11	12	5	56
TMR_00142	tmRNA links to Rfam database...	0.56	0.47	0.67	48	70804	31	9	15	7	54
TMR_00207	tmRNA links to Rfam database...	0.52	0.39	0.70	40	72333	21	4	13	4	63
TMR_00257	tmRNA links to Rfam database...	0.56	0.40	0.78	39	67111	16	3	8	5	59
TMR_00271	tmRNA links to Rfam database...	0.48	0.34	0.69	31	64216	21	7	7	7	60
TMR_00332	tmRNA links to Rfam database...	0.52	0.41	0.66	41	67099	22	6	15	1	58
TMR_00366	tmRNA links to Rfam database...	0.55	0.46	0.65	46	67825	36	12	13	11	54
TMR_00378	tmRNA links to Rfam database...	0.55	0.46	0.65	45	67827	35	8	16	11	52
TMR_00404	tmRNA links to Rfam database...	0.66	0.54	0.81	50	67466	20	4	8	8	42
TMR_00427	tmRNA links to Rfam database...	0.47	0.34	0.65	33	67477	20	7	11	2	64
TMR_00443	tmRNA links to Rfam database...	0.56	0.41	0.75	43	67104	14	6	8	0	61
TMR_00451	tmRNA links to Rfam database...	0.34	0.25	0.47	22	63499	29	10	15	4	67
TMR_00458	tmRNA links to Rfam database...	0.55	0.42	0.72	39	63492	15	7	8	0	54
TMR_00469	tmRNA links to Rfam database...	0.72	0.61	0.86	61	64549	11	4	6	1	39
TMR_00472	tmRNA links to Rfam database...	0.75	0.63	0.88	61	64551	13	2	6	5	36
TMR_00519	tmRNA links to Rfam database...	0.50	0.40	0.62	38	63129	27	14	9	4	57
TMR_00520	tmRNA links to Rfam database...	0.40	0.31	0.52	31	63130	33	12	17	4	68
TMR_00522	tmRNA links to Rfam database...	0.54	0.42	0.68	41	63130	24	9	10	5	56
TMR_00528	tmRNA links to Rfam database...	0.49	0.40	0.59	39	63124	31	12	15	4	58
TMR_00540	tmRNA links to Rfam database...	0.47	0.37	0.59	38	73472	26	10	16	0	66
TMR_00568	tmRNA links to Rfam database...	0.72	0.66	0.78	65	60643	26	2	16	8	34
TMR_00571	tmRNA links to Rfam database...	0.77	0.71	0.83	70	60642	22	2	12	8	29
TMR_00580	tmRNA links to Rfam database...	0.53	0.47	0.59	47	60647	40	3	29	8	53
TMR_00584	tmRNA links to Rfam database...	0.71	0.65	0.79	63	60995	25	3	14	8	34
TMR_00586	tmRNA links to Rfam database...	0.61	0.52	0.72	50	61006	26	5	14	7	47
TMR_00616	tmRNA links to Rfam database...	0.66	0.57	0.77	56	67088	23	3	14	6	43
TMR_00699	tmRNA links to Rfam database...	0.54	0.38	0.76	39	67110	13	3	9	1	63
TMR_00702	tmRNA links to Rfam database...	0.42	0.32	0.56	32	67104	28	3	22	3	68
TMR_00703	tmRNA links to Rfam database...	0.56	0.41	0.76	41	67474	18	3	10	5	58

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Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP	2536
Total TN	4277970
Total FP	6280
Total FP CONTRA	1043
Total FP INCONS	4528
Total FP COMP	709
Total FN	4913

Total Scores
MCC	0.325
Average MCC ± 95% Confidence Intervals	0.328 ± 0.039
Sensitivity	0.340
Positive Predictive Value	0.313
Nr of predictions	78

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00064	RNaseP_bact_a links to Rfam database...	0.19	0.19	0.19	17	45361	82	13	60	9	72
ASE_00090	RNaseP_bact_a links to Rfam database...	0.32	0.33	0.31	33	55504	91	4	70	17	68
ASE_00135	RNaseP_bact_a links to Rfam database...	0.45	0.46	0.45	50	63078	74	12	50	12	59
ASE_00153	RNaseP_nuc links to Rfam database...	0.33	0.38	0.29	28	57534	96	15	53	28	45
ASE_00215	RNaseP_bact_a links to Rfam database...	0.28	0.28	0.29	28	48418	83	6	64	13	71
ASE_00305	RNaseP_bact_b links to Rfam database...	0.15	0.18	0.14	15	54504	107	20	76	11	70
ASE_00328	RNaseP_bact_b links to Rfam database...	0.51	0.49	0.53	55	72667	61	5	44	12	57
ASE_00361	RNaseP_bact_a links to Rfam database...	0.36	0.37	0.35	47	75333	94	11	75	8	80
ASE_00427	RNaseP_nuc links to Rfam database...	0.08	0.11	0.06	5	40673	91	35	42	14	41
ASE_00441	RNaseP_bact_a links to Rfam database...	0.45	0.46	0.45	51	64147	73	3	60	10	61
SRP_00006	Metazoa_SRP links to Rfam database...	0.49	0.49	0.49	49	45654	54	4	46	4	52
SRP_00011	Plant_SRP links to Rfam database...	0.10	0.11	0.09	11	46242	107	10	97	0	93
SRP_00015	Plant_SRP links to Rfam database...	0.30	0.30	0.30	30	46259	73	8	63	2	69
SRP_00024	Bacteria_large_SRP links to Rfam database...	0.51	0.49	0.53	43	37594	49	7	31	11	44
SRP_00026	Bacteria_large_SRP links to Rfam database...	0.68	0.68	0.69	60	36769	45	0	27	18	28
SRP_00030	Bacteria_large_SRP links to Rfam database...	0.30	0.31	0.29	27	36764	69	5	60	4	61
SRP_00031	Bacteria_large_SRP links to Rfam database...	0.64	0.61	0.67	54	36234	37	3	24	10	35
SRP_00037	Bacteria_large_SRP links to Rfam database...	0.17	0.17	0.17	15	36496	80	4	70	6	72
SRP_00050	Metazoa_SRP links to Rfam database...	0.85	0.84	0.86	83	44753	34	0	14	20	16
SRP_00066	Metazoa_SRP links to Rfam database...	0.14	0.14	0.14	14	45349	89	12	76	1	86
SRP_00086	Metazoa_SRP links to Rfam database...	0.62	0.62	0.61	62	44152	51	4	35	12	38
SRP_00088	Bacteria_large_SRP links to Rfam database...	0.38	0.38	0.38	34	34102	62	5	50	7	55
SRP_00089	Bacteria_large_SRP links to Rfam database...	0.66	0.67	0.66	60	35687	39	4	27	8	30
SRP_00090	Bacteria_large_SRP links to Rfam database...	0.41	0.39	0.44	35	35432	51	6	38	7	55
SRP_00102	Metazoa_SRP links to Rfam database...	0.44	0.44	0.45	44	44454	60	4	49	7	57
SRP_00103	Metazoa_SRP links to Rfam database...	0.67	0.68	0.66	69	45346	44	3	33	8	33
SRP_00152	Plant_SRP links to Rfam database...	0.31	0.31	0.32	32	45653	73	9	59	5	71
SRP_00171	Metazoa_SRP links to Rfam database...	0.17	0.19	0.16	17	45343	91	13	78	0	71
SRP_00178	Plant_SRP links to Rfam database...	0.17	0.17	0.18	17	45657	84	9	70	5	85
SRP_00179	Plant_SRP links to Rfam database...	0.03	0.03	0.03	3	45955	98	7	91	0	102
SRP_00181	Plant_SRP links to Rfam database...	0.09	0.09	0.10	9	45963	84	12	72	0	93
SRP_00182	Plant_SRP links to Rfam database...	0.34	0.35	0.34	35	45952	72	13	56	3	66
SRP_00188	Plant_SRP links to Rfam database...	0.26	0.27	0.25	21	31041	64	13	50	1	58
SRP_00228	Metazoa_SRP links to Rfam database...	0.61	0.61	0.62	58	45357	51	9	27	15	37
SRP_00234	Bacteria_large_SRP links to Rfam database...	0.71	0.71	0.71	61	36229	43	4	21	18	25
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.27	0.26	0.27	23	36231	62	13	48	1	65
SRP_00317	Metazoa_SRP links to Rfam database...	0.14	0.14	0.14	14	45051	89	6	79	4	84
SRP_00335	Bacteria_large_SRP links to Rfam database...	0.27	0.38	0.19	15	35166	94	30	34	30	24
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.61	0.60	0.61	55	35421	48	3	32	13	36
SRP_00347	Metazoa_SRP links to Rfam database...	0.64	0.66	0.62	63	46564	51	5	33	13	33
SRP_00368	Metazoa_SRP links to Rfam database...	0.52	0.52	0.52	51	43857	56	5	43	8	47
TMR_00017	tmRNA links to Rfam database...	0.27	0.26	0.27	27	67061	85	12	61	12	75
TMR_00018	tmRNA links to Rfam database...	0.34	0.37	0.32	34	64515	80	23	48	9	58
TMR_00042	tmRNA links to Rfam database...	0.24	0.24	0.24	24	62737	83	11	63	9	74
TMR_00046	tmRNA links to Rfam database...	0.38	0.42	0.35	40	62722	90	15	58	17	56
TMR_00048	tmRNA links to Rfam database...	0.51	0.55	0.47	52	64870	70	16	42	12	43
TMR_00080	tmRNA links to Rfam database...	0.19	0.22	0.17	21	70379	108	32	68	8	75
TMR_00082	tmRNA links to Rfam database...	0.30	0.33	0.28	32	67782	91	23	59	9	64
TMR_00123	tmRNA links to Rfam database...	0.21	0.23	0.21	23	66318	95	16	73	6	78
TMR_00137	tmRNA links to Rfam database...	0.30	0.34	0.27	30	60965	85	25	55	5	59
TMR_00142	tmRNA links to Rfam database...	0.30	0.33	0.28	34	70753	96	25	64	7	68
TMR_00207	tmRNA links to Rfam database...	0.26	0.27	0.25	28	72276	92	17	69	6	75
TMR_00257	tmRNA links to Rfam database...	0.26	0.29	0.24	28	67045	100	17	71	12	70
TMR_00271	tmRNA links to Rfam database...	0.19	0.21	0.18	19	64156	98	18	68	12	72
TMR_00332	tmRNA links to Rfam database...	0.27	0.29	0.25	29	67043	96	21	68	7	70
TMR_00366	tmRNA links to Rfam database...	0.25	0.27	0.23	27	67778	97	19	72	6	73
TMR_00378	tmRNA links to Rfam database...	0.17	0.20	0.15	19	67773	107	29	75	3	78
TMR_00404	tmRNA links to Rfam database...	0.20	0.22	0.18	20	67416	98	13	79	6	72
TMR_00427	tmRNA links to Rfam database...	0.15	0.15	0.14	15	67420	98	21	72	5	82
TMR_00443	tmRNA links to Rfam database...	0.23	0.25	0.22	26	67043	107	10	82	15	78
TMR_00451	tmRNA links to Rfam database...	0.15	0.17	0.13	15	63432	103	35	64	4	74
TMR_00458	tmRNA links to Rfam database...	0.32	0.33	0.30	31	63443	80	16	56	8	62
TMR_00469	tmRNA links to Rfam database...	0.17	0.19	0.16	19	64500	111	14	87	10	81
TMR_00472	tmRNA links to Rfam database...	0.26	0.27	0.25	26	64516	87	16	62	9	71
TMR_00519	tmRNA links to Rfam database...	0.14	0.15	0.13	14	63085	101	22	69	10	81
TMR_00520	tmRNA links to Rfam database...	0.17	0.18	0.16	18	63075	102	28	69	5	81
TMR_00522	tmRNA links to Rfam database...	0.27	0.30	0.24	29	63068	94	31	62	1	68
TMR_00528	tmRNA links to Rfam database...	0.23	0.25	0.22	24	63081	92	28	57	7	73
TMR_00540	tmRNA links to Rfam database...	0.26	0.28	0.24	29	73417	98	15	75	8	75
TMR_00568	tmRNA links to Rfam database...	0.39	0.39	0.39	39	60625	76	15	47	14	60
TMR_00571	tmRNA links to Rfam database...	0.50	0.51	0.50	50	60625	71	7	44	20	49
TMR_00580	tmRNA links to Rfam database...	0.43	0.45	0.41	45	60615	82	7	59	16	55
TMR_00584	tmRNA links to Rfam database...	0.27	0.28	0.26	27	60972	91	13	63	15	70
TMR_00586	tmRNA links to Rfam database...	0.47	0.49	0.44	48	60967	74	19	41	14	49
TMR_00616	tmRNA links to Rfam database...	0.36	0.39	0.34	39	67045	86	14	63	9	60
TMR_00699	tmRNA links to Rfam database...	0.23	0.25	0.22	25	67048	94	15	73	6	77
TMR_00702	tmRNA links to Rfam database...	0.13	0.14	0.12	14	67047	107	9	91	7	86
TMR_00703	tmRNA links to Rfam database...	0.21	0.23	0.20	23	67411	99	22	72	5	76

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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 RNASampler(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RNASampler(20)

2. Individual counts for RNASampler(20) [ download as .csv ]

Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

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