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)		RNAfold
MCC	0.543	>	0.390
Average MCC ± 95% Confidence Intervals	0.539 ± 0.032	>	0.391 ± 0.045
Sensitivity	0.425	>	0.397
Positive Predictive Value	0.695	>	0.386
Total TP	1886	>	1761
Total TN	2904341	>	2902486
Total FP	1026	<	3093
Total FP CONTRA	246	<	484
Total FP INCONS	580	<	2322
Total FP COMP	200	<	287
Total FN	2547	<	2672
P-value	3.56938820447e-08

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Performance plots

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

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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	1886
Total TN	2904341
Total FP	1026
Total FP CONTRA	246
Total FP INCONS	580
Total FP COMP	200
Total FN	2547

Total Scores
MCC	0.543
Average MCC ± 95% Confidence Intervals	0.539 ± 0.032
Sensitivity	0.425
Positive Predictive Value	0.695
Nr of predictions	45

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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
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 RNAfold - scored lower in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP	1761
Total TN	2902486
Total FP	3093
Total FP CONTRA	484
Total FP INCONS	2322
Total FP COMP	287
Total FN	2672

Total Scores
MCC	0.390
Average MCC ± 95% Confidence Intervals	0.391 ± 0.045
Sensitivity	0.397
Positive Predictive Value	0.386
Nr of predictions	45

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2. Individual counts for RNAfold [ 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...	0.43	0.43	0.44	38	45364	53	5	44	4	51
ASE_00090	RNaseP_bact_a links to Rfam database...	0.54	0.54	0.54	55	55509	51	4	43	4	46
ASE_00135	RNaseP_bact_a links to Rfam database...	0.46	0.45	0.47	49	63085	60	8	48	4	60
ASE_00153	RNaseP_nuc links to Rfam database...	0.61	0.62	0.61	45	57556	72	2	27	43	28
ASE_00215	RNaseP_bact_a links to Rfam database...	0.54	0.51	0.57	50	48429	39	4	33	2	49
ASE_00328	RNaseP_bact_b links to Rfam database...	0.41	0.41	0.40	46	72657	74	3	65	6	66
ASE_00361	RNaseP_bact_a links to Rfam database...	0.49	0.46	0.51	59	75351	59	7	49	3	68
ASE_00441	RNaseP_bact_a links to Rfam database...	0.78	0.74	0.81	83	64159	31	3	16	12	29
TMR_00017	tmRNA links to Rfam database...	0.39	0.40	0.38	41	67053	73	15	52	6	61
TMR_00018	tmRNA links to Rfam database...	0.12	0.13	0.12	12	64521	93	11	76	6	80
TMR_00042	tmRNA links to Rfam database...	0.24	0.24	0.24	24	62735	79	9	67	3	74
TMR_00046	tmRNA links to Rfam database...	0.54	0.56	0.53	54	62733	51	11	37	3	42
TMR_00048	tmRNA links to Rfam database...	0.33	0.35	0.31	33	64873	79	9	65	5	62
TMR_00080	tmRNA links to Rfam database...	0.55	0.56	0.53	54	70398	51	16	32	3	42
TMR_00082	tmRNA links to Rfam database...	0.59	0.58	0.59	56	67801	44	12	27	5	40
TMR_00123	tmRNA links to Rfam database...	0.49	0.49	0.51	49	66333	53	10	38	5	52
TMR_00137	tmRNA links to Rfam database...	0.25	0.27	0.24	24	60976	79	19	56	4	65
TMR_00142	tmRNA links to Rfam database...	0.56	0.61	0.53	62	70758	56	22	34	0	40
TMR_00207	tmRNA links to Rfam database...	0.36	0.35	0.36	36	72291	70	5	58	7	67
TMR_00257	tmRNA links to Rfam database...	0.25	0.24	0.26	24	67068	73	8	61	4	74
TMR_00271	tmRNA links to Rfam database...	0.49	0.48	0.50	44	64173	53	9	35	9	47
TMR_00332	tmRNA links to Rfam database...	0.39	0.38	0.39	38	67064	63	10	49	4	61
TMR_00366	tmRNA links to Rfam database...	0.28	0.28	0.28	28	67797	84	12	59	13	72
TMR_00378	tmRNA links to Rfam database...	0.28	0.30	0.27	29	67790	88	7	70	11	68
TMR_00404	tmRNA links to Rfam database...	0.49	0.52	0.46	48	67424	67	10	46	11	44
TMR_00427	tmRNA links to Rfam database...	0.31	0.31	0.31	30	67432	71	11	55	5	67
TMR_00443	tmRNA links to Rfam database...	0.44	0.44	0.44	46	67057	60	14	44	2	58
TMR_00451	tmRNA links to Rfam database...	0.17	0.19	0.16	17	63441	88	16	72	0	72
TMR_00458	tmRNA links to Rfam database...	0.24	0.24	0.24	22	63454	78	7	63	8	71
TMR_00469	tmRNA links to Rfam database...	0.39	0.41	0.38	41	64511	68	11	57	0	59
TMR_00472	tmRNA links to Rfam database...	0.38	0.40	0.36	39	64511	73	24	46	3	58
TMR_00519	tmRNA links to Rfam database...	0.14	0.15	0.13	14	63083	103	16	77	10	81
TMR_00520	tmRNA links to Rfam database...	0.42	0.43	0.41	43	63084	72	17	46	9	56
TMR_00522	tmRNA links to Rfam database...	0.36	0.36	0.36	35	63093	71	11	51	9	62
TMR_00528	tmRNA links to Rfam database...	0.13	0.13	0.12	13	63081	106	12	84	10	84
TMR_00540	tmRNA links to Rfam database...	0.37	0.37	0.37	38	73433	74	8	57	9	66
TMR_00568	tmRNA links to Rfam database...	0.59	0.59	0.60	58	60630	47	3	35	9	41
TMR_00571	tmRNA links to Rfam database...	0.59	0.60	0.58	59	60624	48	8	35	5	40
TMR_00580	tmRNA links to Rfam database...	0.53	0.53	0.54	53	60627	55	15	31	9	47
TMR_00584	tmRNA links to Rfam database...	0.40	0.42	0.38	41	60967	73	8	59	6	56
TMR_00586	tmRNA links to Rfam database...	0.23	0.25	0.21	24	60962	90	19	70	1	73
TMR_00616	tmRNA links to Rfam database...	0.36	0.37	0.36	37	67057	72	18	49	5	62
TMR_00699	tmRNA links to Rfam database...	0.22	0.23	0.22	23	67056	84	11	71	2	79
TMR_00702	tmRNA links to Rfam database...	0.16	0.16	0.16	16	67059	90	10	76	4	84
TMR_00703	tmRNA links to Rfam database...	0.31	0.31	0.30	31	67426	75	14	57	4	68

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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 RNAfold - scored lower in this pairwise comparison

1. Total counts & total scores for RNAfold

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