CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	IPknot		RNASampler(20)
MCC	0.631	>	0.565
Average MCC ± 95% Confidence Intervals	0.622 ± 0.045	>	0.539 ± 0.043
Sensitivity	0.577	>	0.413
Positive Predictive Value	0.690	<	0.772
Total TP	4301	>	3079
Total TN	4279845	<	4282091
Total FP	2302	>	1146
Total FP CONTRA	357	>	258
Total FP INCONS	1574	>	649
Total FP COMP	371	>	239
Total FN	3148	<	4370
P-value	3.56938820447e-08

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Performance plots

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

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Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	4301
Total TN	4279845
Total FP	2302
Total FP CONTRA	357
Total FP INCONS	1574
Total FP COMP	371
Total FN	3148

Total Scores
MCC	0.631
Average MCC ± 95% Confidence Intervals	0.622 ± 0.045
Sensitivity	0.577
Positive Predictive Value	0.690
Nr of predictions	78

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2. Individual counts for IPknot [ 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...	0.68	0.60	0.77	53	45382	22	3	13	6	36
ASE_00090	RNaseP_bact_a links to Rfam database...	0.66	0.58	0.75	59	55532	20	1	19	0	42
ASE_00135	RNaseP_bact_a links to Rfam database...	0.67	0.58	0.79	63	63110	22	1	16	5	46
ASE_00153	RNaseP_nuc links to Rfam database...	0.52	0.51	0.54	37	57562	60	6	25	29	36
ASE_00215	RNaseP_bact_a links to Rfam database...	0.48	0.41	0.56	41	48443	32	1	31	0	58
ASE_00305	RNaseP_bact_b links to Rfam database...	0.73	0.58	0.92	49	54562	9	0	4	5	36
ASE_00328	RNaseP_bact_b links to Rfam database...	0.70	0.60	0.83	67	72690	20	4	10	6	45
ASE_00361	RNaseP_bact_a links to Rfam database...	0.53	0.47	0.59	60	75364	45	9	33	3	67
ASE_00427	RNaseP_nuc links to Rfam database...	0.19	0.20	0.20	9	40709	45	9	28	8	37
ASE_00441	RNaseP_bact_a links to Rfam database...	0.79	0.72	0.86	81	64167	15	2	11	2	31
SRP_00006	Metazoa_SRP links to Rfam database...	0.86	0.86	0.85	87	45651	18	3	12	3	14
SRP_00011	Plant_SRP links to Rfam database...	0.45	0.40	0.51	42	46277	41	1	40	0	62
SRP_00015	Plant_SRP links to Rfam database...	0.83	0.77	0.90	76	46276	10	0	8	2	23
SRP_00024	Bacteria_large_SRP links to Rfam database...	0.55	0.53	0.58	46	37596	33	5	28	0	41
SRP_00026	Bacteria_large_SRP links to Rfam database...	0.79	0.72	0.86	63	36783	16	0	10	6	25
SRP_00030	Bacteria_large_SRP links to Rfam database...	0.79	0.78	0.80	69	36770	17	3	14	0	19
SRP_00031	Bacteria_large_SRP links to Rfam database...	0.64	0.62	0.67	55	36233	28	3	24	1	34
SRP_00037	Bacteria_large_SRP links to Rfam database...	0.64	0.62	0.66	54	36503	28	5	23	0	33
SRP_00050	Metazoa_SRP links to Rfam database...	0.96	0.94	0.98	93	44755	4	0	2	2	6
SRP_00066	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	45364	87	9	78	0	100
SRP_00086	Metazoa_SRP links to Rfam database...	0.91	0.90	0.92	90	44155	10	1	7	2	10
SRP_00088	Bacteria_large_SRP links to Rfam database...	0.69	0.69	0.69	61	34103	27	4	23	0	28
SRP_00089	Bacteria_large_SRP links to Rfam database...	0.89	0.87	0.92	78	35693	7	0	7	0	12
SRP_00090	Bacteria_large_SRP links to Rfam database...	0.85	0.83	0.86	75	35424	14	1	11	2	15
SRP_00102	Metazoa_SRP links to Rfam database...	0.84	0.83	0.85	84	44452	15	3	12	0	17
SRP_00103	Metazoa_SRP links to Rfam database...	0.87	0.84	0.90	86	45355	12	2	8	2	16
SRP_00152	Plant_SRP links to Rfam database...	0.64	0.56	0.73	58	45673	22	2	20	0	45
SRP_00171	Metazoa_SRP links to Rfam database...	0.06	0.06	0.07	5	45376	70	12	58	0	83
SRP_00178	Plant_SRP links to Rfam database...	0.84	0.75	0.95	76	45673	6	0	4	2	26
SRP_00179	Plant_SRP links to Rfam database...	0.65	0.60	0.72	63	45968	28	2	23	3	42
SRP_00181	Plant_SRP links to Rfam database...	0.53	0.44	0.63	45	45985	26	0	26	0	57
SRP_00182	Plant_SRP links to Rfam database...	0.75	0.73	0.76	74	45959	25	3	20	2	27
SRP_00188	Plant_SRP links to Rfam database...	0.21	0.22	0.21	17	31044	64	6	58	0	62
SRP_00228	Metazoa_SRP links to Rfam database...	0.97	0.97	0.98	92	45357	7	0	2	5	3
SRP_00234	Bacteria_large_SRP links to Rfam database...	0.85	0.84	0.86	72	36231	16	0	12	4	14
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.74	0.68	0.81	60	36241	15	6	8	1	28
SRP_00317	Metazoa_SRP links to Rfam database...	0.96	0.93	0.99	91	45058	8	0	1	7	7
SRP_00335	Bacteria_large_SRP links to Rfam database...	0.32	0.44	0.23	17	35172	76	26	30	20	22
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.76	0.74	0.78	67	35425	21	3	16	2	24
SRP_00347	Metazoa_SRP links to Rfam database...	0.78	0.78	0.79	75	46570	23	5	15	3	21
SRP_00368	Metazoa_SRP links to Rfam database...	0.93	0.94	0.93	92	43857	7	4	3	0	6
TMR_00017	tmRNA links to Rfam database...	0.70	0.55	0.89	56	67098	11	0	7	4	46
TMR_00018	tmRNA links to Rfam database...	0.40	0.33	0.48	30	64558	36	6	26	4	62
TMR_00042	tmRNA links to Rfam database...	0.38	0.34	0.44	33	62760	45	2	40	3	65
TMR_00046	tmRNA links to Rfam database...	0.50	0.48	0.53	46	62748	45	5	36	4	50
TMR_00048	tmRNA links to Rfam database...	0.49	0.48	0.50	46	64888	54	6	40	8	49
TMR_00080	tmRNA links to Rfam database...	0.65	0.60	0.70	58	70417	26	6	19	1	38
TMR_00082	tmRNA links to Rfam database...	0.78	0.77	0.80	74	67803	24	8	11	5	22
TMR_00123	tmRNA links to Rfam database...	0.85	0.77	0.93	78	66346	11	0	6	5	23
TMR_00137	tmRNA links to Rfam database...	0.34	0.28	0.40	25	61013	45	6	31	8	64
TMR_00142	tmRNA links to Rfam database...	0.65	0.63	0.67	64	70780	39	9	23	7	38
TMR_00207	tmRNA links to Rfam database...	0.47	0.40	0.56	41	72317	36	3	29	4	62
TMR_00257	tmRNA links to Rfam database...	0.63	0.50	0.80	49	67100	18	2	10	6	49
TMR_00271	tmRNA links to Rfam database...	0.62	0.56	0.68	51	64186	35	6	18	11	40
TMR_00332	tmRNA links to Rfam database...	0.61	0.46	0.81	46	67104	16	0	11	5	53
TMR_00366	tmRNA links to Rfam database...	0.63	0.53	0.76	53	67826	28	5	12	11	47
TMR_00378	tmRNA links to Rfam database...	0.32	0.28	0.38	27	67824	56	14	31	11	70
TMR_00404	tmRNA links to Rfam database...	0.60	0.55	0.65	51	67450	38	6	21	11	41
TMR_00427	tmRNA links to Rfam database...	0.60	0.52	0.69	50	67456	27	10	12	5	47
TMR_00443	tmRNA links to Rfam database...	0.65	0.55	0.77	57	67087	24	8	9	7	47
TMR_00451	tmRNA links to Rfam database...	0.26	0.26	0.27	23	63461	66	16	46	4	66
TMR_00458	tmRNA links to Rfam database...	0.48	0.40	0.59	37	63483	33	6	20	7	56
TMR_00469	tmRNA links to Rfam database...	0.52	0.51	0.54	51	64525	48	16	28	4	49
TMR_00472	tmRNA links to Rfam database...	0.55	0.44	0.67	43	64556	26	6	15	5	54
TMR_00519	tmRNA links to Rfam database...	0.44	0.35	0.57	33	63132	35	7	18	10	62
TMR_00520	tmRNA links to Rfam database...	0.52	0.46	0.58	46	63110	43	7	27	9	53
TMR_00522	tmRNA links to Rfam database...	0.53	0.47	0.60	46	63113	39	5	26	8	51
TMR_00528	tmRNA links to Rfam database...	0.43	0.40	0.46	39	63106	55	11	34	10	58
TMR_00540	tmRNA links to Rfam database...	0.70	0.63	0.79	65	73454	27	6	11	10	39
TMR_00568	tmRNA links to Rfam database...	0.66	0.53	0.84	52	60664	16	0	10	6	47
TMR_00571	tmRNA links to Rfam database...	0.68	0.60	0.79	59	60651	24	2	14	8	40
TMR_00580	tmRNA links to Rfam database...	0.74	0.71	0.77	71	60634	29	2	19	8	29
TMR_00584	tmRNA links to Rfam database...	0.61	0.59	0.64	57	60986	36	3	29	4	40
TMR_00586	tmRNA links to Rfam database...	0.58	0.53	0.65	51	60996	34	6	22	6	46
TMR_00616	tmRNA links to Rfam database...	0.53	0.45	0.62	45	67088	33	6	22	5	54
TMR_00699	tmRNA links to Rfam database...	0.80	0.72	0.89	73	67079	13	3	6	4	29
TMR_00702	tmRNA links to Rfam database...	0.58	0.48	0.70	48	67092	26	5	16	5	52
TMR_00703	tmRNA links to Rfam database...	0.53	0.45	0.61	45	67454	34	3	26	5	54

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

1. Total counts & total scores for IPknot

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

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

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

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