CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(20)		RNASampler(20)
MCC	0.632	>	0.553
Average MCC ± 95% Confidence Intervals	0.645 ± 0.031	>	0.570 ± 0.039
Sensitivity	0.526	>	0.434
Positive Predictive Value	0.760	>	0.705
Total TP	2401	>	1981
Total TN	2918628	<	2918978
Total FP	911	<	1029
Total FP CONTRA	208	<	247
Total FP INCONS	549	<	580
Total FP COMP	154	<	202
Total FN	2165	<	2585
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	2401
Total TN	2918628
Total FP	911
Total FP CONTRA	208
Total FP INCONS	549
Total FP COMP	154
Total FN	2165

Total Scores
MCC	0.632
Average MCC ± 95% Confidence Intervals	0.645 ± 0.031
Sensitivity	0.526
Positive Predictive Value	0.760
Nr of predictions	50

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2. Individual counts for RNAalifold(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...	0.72	0.61	0.84	54	45387	13	0	10	3	35
ASE_00090	RNaseP_bact_a links to Rfam database...	0.72	0.55	0.93	56	55551	4	0	4	0	45
ASE_00135	RNaseP_bact_a links to Rfam database...	0.49	0.38	0.63	41	63125	24	1	23	0	68
ASE_00153	RNaseP_nuc links to Rfam database...	0.41	0.34	0.50	25	57580	28	1	24	3	48
ASE_00215	RNaseP_bact_a links to Rfam database...	0.69	0.49	0.96	49	48465	2	2	0	0	50
ASE_00328	RNaseP_bact_b links to Rfam database...	0.71	0.64	0.77	72	72678	27	5	16	6	40
ASE_00361	RNaseP_bact_a links to Rfam database...	0.69	0.51	0.93	65	75396	5	1	4	0	62
ASE_00441	RNaseP_bact_a links to Rfam database...	0.55	0.38	0.80	43	64207	15	0	11	4	69
PDB_00571	tRNA links to Rfam database...	0.87	0.80	0.95	20	3300	1	1	0	0	5
PDB_00828	Purine links to Rfam database...	0.84	0.70	1.00	19	2466	0	0	0	0	8
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01073	SAM links to Rfam database...	0.80	0.65	1.00	22	4349	1	0	0	1	12
TMR_00017	tmRNA links to Rfam database...	0.68	0.54	0.85	55	67096	14	0	10	4	47
TMR_00018	tmRNA links to Rfam database...	0.62	0.53	0.72	49	64552	23	7	12	4	43
TMR_00042	tmRNA links to Rfam database...	0.68	0.53	0.87	52	62775	9	1	7	1	46
TMR_00046	tmRNA links to Rfam database...	0.56	0.49	0.64	47	62761	28	4	23	1	49
TMR_00048	tmRNA links to Rfam database...	0.64	0.52	0.80	49	64919	13	5	7	1	46
TMR_00080	tmRNA links to Rfam database...	0.57	0.50	0.64	48	70425	33	8	19	6	48
TMR_00082	tmRNA links to Rfam database...	0.59	0.50	0.69	48	67826	28	11	11	6	48
TMR_00123	tmRNA links to Rfam database...	0.70	0.55	0.89	56	66367	12	1	6	5	45
TMR_00137	tmRNA links to Rfam database...	0.56	0.48	0.66	43	61010	24	11	11	2	46
TMR_00142	tmRNA links to Rfam database...	0.63	0.52	0.77	53	70807	22	4	12	6	49
TMR_00207	tmRNA links to Rfam database...	0.66	0.54	0.81	56	72321	19	7	6	6	47
TMR_00257	tmRNA links to Rfam database...	0.75	0.63	0.89	62	67091	15	4	4	7	36
TMR_00271	tmRNA links to Rfam database...	0.48	0.37	0.63	34	64207	26	5	15	6	57
TMR_00332	tmRNA links to Rfam database...	0.64	0.52	0.78	51	67096	19	1	13	5	48
TMR_00366	tmRNA links to Rfam database...	0.55	0.48	0.62	48	67819	29	8	21	0	52
TMR_00378	tmRNA links to Rfam database...	0.49	0.41	0.59	40	67828	29	8	20	1	57
TMR_00404	tmRNA links to Rfam database...	0.56	0.47	0.68	43	67465	20	3	17	0	49
TMR_00427	tmRNA links to Rfam database...	0.50	0.36	0.69	35	67477	16	7	9	0	62
TMR_00443	tmRNA links to Rfam database...	0.73	0.63	0.86	65	67085	15	6	5	4	39
TMR_00451	tmRNA links to Rfam database...	0.57	0.51	0.65	45	63477	30	10	14	6	44
TMR_00458	tmRNA links to Rfam database...	0.54	0.46	0.64	43	63479	28	8	16	4	50
TMR_00469	tmRNA links to Rfam database...	0.70	0.60	0.81	60	64546	14	7	7	0	40
TMR_00472	tmRNA links to Rfam database...	0.65	0.56	0.75	54	64548	19	8	10	1	43
TMR_00519	tmRNA links to Rfam database...	0.57	0.48	0.67	46	63121	25	7	16	2	49
TMR_00520	tmRNA links to Rfam database...	0.53	0.43	0.65	43	63124	27	8	15	4	56
TMR_00522	tmRNA links to Rfam database...	0.52	0.42	0.64	41	63126	27	6	17	4	56
TMR_00528	tmRNA links to Rfam database...	0.54	0.47	0.62	46	63116	34	9	19	6	51
TMR_00540	tmRNA links to Rfam database...	0.66	0.54	0.81	56	73467	17	5	8	4	48
TMR_00568	tmRNA links to Rfam database...	0.73	0.67	0.80	66	60644	22	3	13	6	33
TMR_00571	tmRNA links to Rfam database...	0.75	0.69	0.83	68	60644	20	3	11	6	31
TMR_00580	tmRNA links to Rfam database...	0.74	0.65	0.83	65	60648	19	1	12	6	35
TMR_00584	tmRNA links to Rfam database...	0.75	0.68	0.83	66	60995	17	2	12	3	31
TMR_00586	tmRNA links to Rfam database...	0.69	0.64	0.76	62	60993	26	8	12	6	35
TMR_00616	tmRNA links to Rfam database...	0.64	0.55	0.76	54	67090	17	7	10	0	45
TMR_00699	tmRNA links to Rfam database...	0.68	0.54	0.85	55	67096	15	1	9	5	47
TMR_00702	tmRNA links to Rfam database...	0.54	0.43	0.68	43	67098	24	2	18	4	57
TMR_00703	tmRNA links to Rfam database...	0.67	0.54	0.83	53	67464	15	1	10	4	46

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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	1981
Total TN	2918978
Total FP	1029
Total FP CONTRA	247
Total FP INCONS	580
Total FP COMP	202
Total FN	2585

Total Scores
MCC	0.553
Average MCC ± 95% Confidence Intervals	0.570 ± 0.039
Sensitivity	0.434
Positive Predictive Value	0.705
Nr of predictions	50

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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_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_00441	RNaseP_bact_a links to Rfam database...	0.46	0.31	0.69	35	64210	16	0	16	0	77
PDB_00571	tRNA links to Rfam database...	0.87	0.80	0.95	20	3300	1	1	0	0	5
PDB_00828	Purine links to Rfam database...	0.86	0.74	1.00	20	2465	0	0	0	0	7
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01073	SAM links to Rfam database...	0.77	0.59	1.00	20	4351	1	0	0	1	14
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 RNAalifold(20) - scored higher in this pairwise comparison

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

2. Individual counts for RNAalifold(20) [ 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 ]