CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	TurboFold(20)		RNASampler(20)
MCC	0.668	>	0.553
Average MCC ± 95% Confidence Intervals	0.682 ± 0.032	>	0.570 ± 0.039
Sensitivity	0.614	>	0.434
Positive Predictive Value	0.727	>	0.705
Total TP	2805	>	1981
Total TN	2917930	<	2918978
Total FP	1409	>	1029
Total FP CONTRA	229	<	247
Total FP INCONS	822	>	580
Total FP COMP	358	>	202
Total FN	1761	<	2585
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	2805
Total TN	2917930
Total FP	1409
Total FP CONTRA	229
Total FP INCONS	822
Total FP COMP	358
Total FN	1761

Total Scores
MCC	0.668
Average MCC ± 95% Confidence Intervals	0.682 ± 0.032
Sensitivity	0.614
Positive Predictive Value	0.727
Nr of predictions	50

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2. Individual counts for TurboFold(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...	0.78	0.71	0.85	63	45377	19	0	11	8	26
ASE_00090	RNaseP_bact_a links to Rfam database...	0.69	0.66	0.72	67	55518	31	1	25	5	34
ASE_00135	RNaseP_bact_a links to Rfam database...	0.77	0.71	0.84	77	63098	26	0	15	11	32
ASE_00153	RNaseP_nuc links to Rfam database...	0.67	0.67	0.67	49	57557	63	2	22	39	24
ASE_00215	RNaseP_bact_a links to Rfam database...	0.65	0.55	0.78	54	48447	23	0	15	8	45
ASE_00328	RNaseP_bact_b links to Rfam database...	0.74	0.63	0.86	71	72688	24	1	11	12	41
ASE_00361	RNaseP_bact_a links to Rfam database...	0.63	0.54	0.73	68	75373	26	0	25	1	59
ASE_00441	RNaseP_bact_a links to Rfam database...	0.78	0.69	0.89	77	64174	11	0	10	1	35
PDB_00571	tRNA links to Rfam database...	0.85	0.76	0.95	19	3301	1	1	0	0	6
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...	0.86	0.74	1.00	25	4346	1	0	0	1	9
TMR_00017	tmRNA links to Rfam database...	0.60	0.55	0.67	56	67077	32	7	21	4	46
TMR_00018	tmRNA links to Rfam database...	0.49	0.49	0.49	45	64529	50	12	34	4	47
TMR_00042	tmRNA links to Rfam database...	0.74	0.69	0.78	68	62748	25	2	17	6	30
TMR_00046	tmRNA links to Rfam database...	0.64	0.60	0.67	58	62749	34	4	24	6	38
TMR_00048	tmRNA links to Rfam database...	0.68	0.66	0.71	63	64891	35	6	20	9	32
TMR_00080	tmRNA links to Rfam database...	0.64	0.53	0.76	51	70433	16	6	10	0	45
TMR_00082	tmRNA links to Rfam database...	0.63	0.54	0.73	52	67825	20	6	13	1	44
TMR_00123	tmRNA links to Rfam database...	0.66	0.60	0.72	61	66345	29	3	21	5	40
TMR_00137	tmRNA links to Rfam database...	0.52	0.47	0.57	42	61001	37	9	23	5	47
TMR_00142	tmRNA links to Rfam database...	0.66	0.65	0.67	66	70778	40	8	24	8	36
TMR_00207	tmRNA links to Rfam database...	0.50	0.47	0.53	48	72300	47	8	34	5	55
TMR_00257	tmRNA links to Rfam database...	0.68	0.59	0.78	58	67087	22	1	15	6	40
TMR_00271	tmRNA links to Rfam database...	0.65	0.62	0.69	56	64180	34	6	19	9	35
TMR_00332	tmRNA links to Rfam database...	0.58	0.55	0.63	54	67075	37	5	27	5	45
TMR_00366	tmRNA links to Rfam database...	0.79	0.76	0.83	76	67804	27	3	13	11	24
TMR_00378	tmRNA links to Rfam database...	0.77	0.75	0.79	73	67804	32	4	15	13	24
TMR_00404	tmRNA links to Rfam database...	0.67	0.66	0.68	61	67438	45	7	22	16	31
TMR_00427	tmRNA links to Rfam database...	0.67	0.60	0.74	58	67450	25	8	12	5	39
TMR_00443	tmRNA links to Rfam database...	0.61	0.57	0.66	59	67071	35	5	26	4	45
TMR_00451	tmRNA links to Rfam database...	0.49	0.46	0.53	41	63469	40	11	25	4	48
TMR_00458	tmRNA links to Rfam database...	0.56	0.49	0.63	46	63473	30	8	19	3	47
TMR_00469	tmRNA links to Rfam database...	0.78	0.74	0.83	74	64531	24	5	10	9	26
TMR_00472	tmRNA links to Rfam database...	0.79	0.73	0.85	71	64536	24	7	6	11	26
TMR_00519	tmRNA links to Rfam database...	0.52	0.48	0.56	46	63108	47	11	25	11	49
TMR_00520	tmRNA links to Rfam database...	0.51	0.48	0.54	48	63101	51	14	27	10	51
TMR_00522	tmRNA links to Rfam database...	0.55	0.52	0.60	50	63106	43	11	23	9	47
TMR_00528	tmRNA links to Rfam database...	0.54	0.52	0.57	50	63102	48	12	26	10	47
TMR_00540	tmRNA links to Rfam database...	0.49	0.44	0.53	46	73450	47	9	31	7	58
TMR_00568	tmRNA links to Rfam database...	0.77	0.69	0.86	68	60647	21	1	10	10	31
TMR_00571	tmRNA links to Rfam database...	0.78	0.73	0.84	72	60640	27	2	12	13	27
TMR_00580	tmRNA links to Rfam database...	0.78	0.73	0.84	73	60639	26	3	11	12	27
TMR_00584	tmRNA links to Rfam database...	0.78	0.71	0.86	69	60995	21	3	8	10	28
TMR_00586	tmRNA links to Rfam database...	0.74	0.70	0.78	68	60988	28	6	13	9	29
TMR_00616	tmRNA links to Rfam database...	0.77	0.72	0.83	71	67075	21	4	11	6	28
TMR_00699	tmRNA links to Rfam database...	0.66	0.58	0.76	59	67083	24	1	18	5	43
TMR_00702	tmRNA links to Rfam database...	0.60	0.51	0.71	51	67089	26	5	16	5	49
TMR_00703	tmRNA links to Rfam database...	0.81	0.73	0.90	72	67448	13	1	7	5	27

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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 TurboFold(20) - scored higher in this pairwise comparison

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

2. Individual counts for TurboFold(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 ]