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)		CMfinder(20)
MCC	0.565	>	0.413
Average MCC ± 95% Confidence Intervals	0.539 ± 0.043	>	0.403 ± 0.031
Sensitivity	0.413	>	0.258
Positive Predictive Value	0.772	>	0.663
Total TP	3079	>	1920
Total TN	4282091	<	4283181
Total FP	1146	<	1198
Total FP CONTRA	258	>	128
Total FP INCONS	649	<	848
Total FP COMP	239	>	222
Total FN	4370	<	5529
P-value	3.56938820447e-08

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Performance plots

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

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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 CMfinder(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	1920
Total TN	4283181
Total FP	1198
Total FP CONTRA	128
Total FP INCONS	848
Total FP COMP	222
Total FN	5529

Total Scores
MCC	0.413
Average MCC ± 95% Confidence Intervals	0.403 ± 0.031
Sensitivity	0.258
Positive Predictive Value	0.663
Nr of predictions	78

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2. Individual counts for CMfinder(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...	0.48	0.30	0.75	27	45415	10	1	8	1	62
ASE_00090	RNaseP_bact_a links to Rfam database...	0.46	0.33	0.66	33	55561	18	0	17	1	68
ASE_00135	RNaseP_bact_a links to Rfam database...	0.47	0.34	0.65	37	63133	20	1	19	0	72
ASE_00153	RNaseP_nuc links to Rfam database...	0.09	0.05	0.16	4	57605	39	5	16	18	69
ASE_00215	RNaseP_bact_a links to Rfam database...	0.42	0.27	0.66	27	48475	15	0	14	1	72
ASE_00305	RNaseP_bact_b links to Rfam database...	0.52	0.39	0.70	33	54568	15	1	13	1	52
ASE_00328	RNaseP_bact_b links to Rfam database...	0.48	0.34	0.69	38	72716	20	4	13	3	74
ASE_00361	RNaseP_bact_a links to Rfam database...	0.40	0.21	0.75	27	75430	10	1	8	1	100
ASE_00427	RNaseP_nuc links to Rfam database...	0.37	0.30	0.45	14	40724	41	4	13	24	32
ASE_00441	RNaseP_bact_a links to Rfam database...	0.53	0.36	0.80	40	64211	11	1	9	1	72
SRP_00006	Metazoa_SRP links to Rfam database...	0.43	0.29	0.64	29	45708	16	0	16	0	72
SRP_00011	Plant_SRP links to Rfam database...	0.65	0.48	0.88	50	46303	7	0	7	0	54
SRP_00015	Plant_SRP links to Rfam database...	0.53	0.36	0.78	36	46314	10	0	10	0	63
SRP_00024	Bacteria_large_SRP links to Rfam database...	0.55	0.34	0.88	30	37641	4	0	4	0	57
SRP_00026	Bacteria_large_SRP links to Rfam database...	0.43	0.26	0.72	23	36824	9	1	8	0	65
SRP_00030	Bacteria_large_SRP links to Rfam database...	0.11	0.03	0.33	3	36847	6	0	6	0	85
SRP_00031	Bacteria_large_SRP links to Rfam database...	0.39	0.24	0.64	21	36282	12	1	11	0	68
SRP_00037	Bacteria_large_SRP links to Rfam database...	0.26	0.07	1.00	6	36579	0	0	0	0	81
SRP_00050	Metazoa_SRP links to Rfam database...	0.40	0.25	0.64	25	44811	14	2	12	0	74
SRP_00066	Metazoa_SRP links to Rfam database...	0.65	0.45	0.94	45	45403	3	0	3	0	55
SRP_00086	Metazoa_SRP links to Rfam database...	0.68	0.46	1.00	46	44207	0	0	0	0	54
SRP_00088	Bacteria_large_SRP links to Rfam database...	0.29	0.19	0.44	17	34152	22	2	20	0	72
SRP_00089	Bacteria_large_SRP links to Rfam database...	0.45	0.21	0.95	19	35758	1	0	1	0	71
SRP_00090	Bacteria_large_SRP links to Rfam database...	0.46	0.22	0.95	20	35490	1	0	1	0	70
SRP_00102	Metazoa_SRP links to Rfam database...	0.23	0.16	0.35	16	44505	30	3	27	0	85
SRP_00103	Metazoa_SRP links to Rfam database...	0.31	0.23	0.42	23	45396	32	0	32	0	79
SRP_00152	Plant_SRP links to Rfam database...	0.46	0.38	0.57	39	45684	30	6	24	0	64
SRP_00171	Metazoa_SRP links to Rfam database...	0.47	0.34	0.65	30	45405	16	0	16	0	58
SRP_00178	Plant_SRP links to Rfam database...	0.55	0.40	0.75	41	45698	14	4	10	0	61
SRP_00179	Plant_SRP links to Rfam database...	0.59	0.42	0.85	44	46004	8	1	7	0	61
SRP_00181	Plant_SRP links to Rfam database...	0.80	0.67	0.96	68	45985	5	0	3	2	34
SRP_00182	Plant_SRP links to Rfam database...	0.52	0.38	0.73	38	46004	14	0	14	0	63
SRP_00188	Plant_SRP links to Rfam database...	0.52	0.42	0.65	33	31074	18	3	15	0	46
SRP_00228	Metazoa_SRP links to Rfam database...	0.67	0.48	0.92	46	45401	4	1	3	0	49
SRP_00234	Bacteria_large_SRP links to Rfam database...	0.19	0.03	1.00	3	36312	0	0	0	0	83
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.41	0.26	0.66	23	36280	12	1	11	0	65
SRP_00317	Metazoa_SRP links to Rfam database...	0.63	0.43	0.93	42	45105	3	0	3	0	56
SRP_00335	Bacteria_large_SRP links to Rfam database...	0.52	0.44	0.63	17	35218	15	4	6	5	22
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.44	0.30	0.66	27	35470	15	3	11	1	64
SRP_00347	Metazoa_SRP links to Rfam database...	0.32	0.21	0.49	20	46624	21	3	18	0	76
SRP_00368	Metazoa_SRP links to Rfam database...	0.26	0.17	0.40	17	43913	26	3	23	0	81
TMR_00017	tmRNA links to Rfam database...	0.44	0.23	0.85	23	67134	8	0	4	4	79
TMR_00018	tmRNA links to Rfam database...	0.29	0.13	0.67	12	64602	10	0	6	4	80
TMR_00042	tmRNA links to Rfam database...	0.22	0.12	0.40	12	62805	21	0	18	3	86
TMR_00046	tmRNA links to Rfam database...	0.31	0.22	0.44	21	62787	30	4	23	3	75
TMR_00048	tmRNA links to Rfam database...	0.28	0.20	0.40	19	64933	33	5	23	5	76
TMR_00080	tmRNA links to Rfam database...	0.47	0.29	0.76	28	70463	9	0	9	0	68
TMR_00082	tmRNA links to Rfam database...	0.44	0.30	0.63	29	67850	21	1	16	4	67
TMR_00123	tmRNA links to Rfam database...	0.41	0.22	0.76	22	66401	12	0	7	5	79
TMR_00137	tmRNA links to Rfam database...	0.33	0.20	0.55	18	61042	21	2	13	6	71
TMR_00142	tmRNA links to Rfam database...	0.12	0.07	0.21	7	70843	33	8	18	7	95
TMR_00207	tmRNA links to Rfam database...	0.32	0.18	0.54	19	72355	16	6	10	0	84
TMR_00257	tmRNA links to Rfam database...	0.46	0.29	0.76	28	67124	14	0	9	5	70
TMR_00271	tmRNA links to Rfam database...	0.28	0.14	0.57	13	64238	15	1	9	5	78
TMR_00332	tmRNA links to Rfam database...	0.40	0.22	0.71	22	67130	14	0	9	5	77
TMR_00366	tmRNA links to Rfam database...	0.32	0.17	0.59	17	67867	23	3	9	11	83
TMR_00378	tmRNA links to Rfam database...	0.32	0.18	0.59	17	67867	23	3	9	11	80
TMR_00404	tmRNA links to Rfam database...	0.21	0.11	0.42	10	67504	25	4	10	11	82
TMR_00427	tmRNA links to Rfam database...	0.55	0.32	0.94	31	67495	7	0	2	5	66
TMR_00443	tmRNA links to Rfam database...	0.41	0.27	0.64	28	67117	20	1	15	4	76
TMR_00451	tmRNA links to Rfam database...	0.17	0.11	0.25	10	63506	34	6	24	4	79
TMR_00458	tmRNA links to Rfam database...	0.18	0.09	0.38	8	63525	16	1	12	3	85
TMR_00469	tmRNA links to Rfam database...	0.50	0.31	0.79	31	64581	12	1	7	4	69
TMR_00472	tmRNA links to Rfam database...	0.50	0.30	0.83	29	64585	10	1	5	4	68
TMR_00519	tmRNA links to Rfam database...	0.28	0.18	0.44	17	63151	27	2	20	5	78
TMR_00520	tmRNA links to Rfam database...	0.34	0.19	0.59	19	63158	13	4	9	0	80
TMR_00522	tmRNA links to Rfam database...	0.38	0.20	0.73	19	63164	7	1	6	0	78
TMR_00528	tmRNA links to Rfam database...	0.40	0.23	0.71	22	63159	13	2	7	4	75
TMR_00540	tmRNA links to Rfam database...	0.30	0.18	0.50	19	73498	24	2	17	5	85
TMR_00568	tmRNA links to Rfam database...	0.33	0.17	0.65	17	60700	14	0	9	5	82
TMR_00571	tmRNA links to Rfam database...	0.37	0.19	0.70	19	60699	13	0	8	5	80
TMR_00580	tmRNA links to Rfam database...	0.35	0.19	0.66	19	60697	15	2	8	5	81
TMR_00584	tmRNA links to Rfam database...	0.31	0.15	0.63	15	61051	15	1	8	6	82
TMR_00586	tmRNA links to Rfam database...	0.36	0.20	0.68	19	61047	14	1	8	5	78
TMR_00616	tmRNA links to Rfam database...	0.46	0.28	0.76	28	67124	12	3	6	3	71
TMR_00699	tmRNA links to Rfam database...	0.32	0.17	0.61	17	67133	12	3	8	1	85
TMR_00702	tmRNA links to Rfam database...	0.42	0.24	0.73	24	67128	10	3	6	1	76
TMR_00703	tmRNA links to Rfam database...	0.52	0.35	0.78	35	67483	15	1	9	5	64

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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 CMfinder(20) - scored lower in this pairwise comparison

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

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