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)		ProbKnot
MCC	0.553	>	0.469
Average MCC ± 95% Confidence Intervals	0.570 ± 0.039	>	0.494 ± 0.051
Sensitivity	0.434	<	0.467
Positive Predictive Value	0.705	>	0.473
Total TP	1981	<	2134
Total TN	2918978	>	2917277
Total FP	1029	<	2761
Total FP CONTRA	247	<	507
Total FP INCONS	580	<	1868
Total FP COMP	202	<	386
Total FN	2585	>	2432
P-value	3.56938820447e-08

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Performance plots

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

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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	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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Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	2134
Total TN	2917277
Total FP	2761
Total FP CONTRA	507
Total FP INCONS	1868
Total FP COMP	386
Total FN	2432

Total Scores
MCC	0.469
Average MCC ± 95% Confidence Intervals	0.494 ± 0.051
Sensitivity	0.467
Positive Predictive Value	0.473
Nr of predictions	50

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2. Individual counts for ProbKnot [ 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...	0.38	0.39	0.38	35	45358	67	6	52	9	54
ASE_00090	RNaseP_bact_a links to Rfam database...	0.67	0.67	0.66	68	55508	43	4	31	8	33
ASE_00135	RNaseP_bact_a links to Rfam database...	0.65	0.64	0.66	70	63084	43	1	35	7	39
ASE_00153	RNaseP_nuc links to Rfam database...	0.62	0.67	0.58	49	57545	73	9	27	37	24
ASE_00215	RNaseP_bact_a links to Rfam database...	0.60	0.58	0.63	57	48426	35	5	28	2	42
ASE_00328	RNaseP_bact_b links to Rfam database...	0.68	0.66	0.70	74	72665	43	7	25	11	38
ASE_00361	RNaseP_bact_a links to Rfam database...	0.54	0.54	0.54	69	75338	62	13	46	3	58
ASE_00441	RNaseP_bact_a links to Rfam database...	0.78	0.74	0.82	83	64160	27	2	16	9	29
PDB_00571	tRNA links to Rfam database...	0.60	0.60	0.60	15	3296	10	6	4	0	10
PDB_00828	Purine links to Rfam database...	0.86	0.78	0.95	21	2463	1	0	1	0	6
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...	0.50	0.49	0.51	50	67062	55	11	38	6	52
TMR_00018	tmRNA links to Rfam database...	0.34	0.36	0.32	33	64516	76	17	54	5	59
TMR_00042	tmRNA links to Rfam database...	0.34	0.35	0.33	34	62733	71	6	62	3	64
TMR_00046	tmRNA links to Rfam database...	0.27	0.28	0.27	27	62734	81	11	63	7	69
TMR_00048	tmRNA links to Rfam database...	0.26	0.27	0.24	26	64873	87	15	66	6	69
TMR_00080	tmRNA links to Rfam database...	0.39	0.40	0.38	38	70401	62	18	43	1	58
TMR_00082	tmRNA links to Rfam database...	0.69	0.71	0.67	68	67795	38	16	17	5	28
TMR_00123	tmRNA links to Rfam database...	0.46	0.48	0.45	48	66324	63	13	45	5	53
TMR_00137	tmRNA links to Rfam database...	0.24	0.25	0.24	22	60983	79	12	58	9	67
TMR_00142	tmRNA links to Rfam database...	0.55	0.56	0.55	57	70772	62	10	37	15	45
TMR_00207	tmRNA links to Rfam database...	0.34	0.35	0.33	36	72280	79	10	64	5	67
TMR_00257	tmRNA links to Rfam database...	0.12	0.11	0.13	11	67074	81	6	70	5	87
TMR_00271	tmRNA links to Rfam database...	0.59	0.56	0.61	51	64178	43	9	23	11	40
TMR_00332	tmRNA links to Rfam database...	0.53	0.51	0.55	50	67070	47	10	31	6	49
TMR_00366	tmRNA links to Rfam database...	0.57	0.55	0.59	55	67803	49	8	30	11	45
TMR_00378	tmRNA links to Rfam database...	0.26	0.28	0.25	27	67786	94	24	59	11	70
TMR_00404	tmRNA links to Rfam database...	0.36	0.40	0.33	37	67416	86	29	46	11	55
TMR_00427	tmRNA links to Rfam database...	0.46	0.44	0.48	43	67439	54	11	35	8	54
TMR_00443	tmRNA links to Rfam database...	0.50	0.48	0.53	50	67066	52	13	32	7	54
TMR_00451	tmRNA links to Rfam database...	0.18	0.19	0.17	17	63445	88	21	63	4	72
TMR_00458	tmRNA links to Rfam database...	0.46	0.44	0.47	41	63459	54	11	35	8	52
TMR_00469	tmRNA links to Rfam database...	0.51	0.53	0.50	53	64514	57	18	35	4	47
TMR_00472	tmRNA links to Rfam database...	0.46	0.45	0.46	44	64524	64	10	42	12	53
TMR_00519	tmRNA links to Rfam database...	0.40	0.38	0.42	36	63105	64	10	39	15	59
TMR_00520	tmRNA links to Rfam database...	0.51	0.49	0.52	49	63096	56	15	30	11	50
TMR_00522	tmRNA links to Rfam database...	0.39	0.39	0.38	38	63091	70	16	45	9	59
TMR_00528	tmRNA links to Rfam database...	0.30	0.29	0.31	28	63099	73	18	45	10	69
TMR_00540	tmRNA links to Rfam database...	0.36	0.35	0.37	36	73438	74	14	48	12	68
TMR_00568	tmRNA links to Rfam database...	0.31	0.30	0.31	30	60629	73	6	61	6	69
TMR_00571	tmRNA links to Rfam database...	0.62	0.61	0.64	60	60632	46	6	28	12	39
TMR_00580	tmRNA links to Rfam database...	0.69	0.66	0.72	66	60634	37	3	23	11	34
TMR_00584	tmRNA links to Rfam database...	0.58	0.57	0.59	55	60982	53	5	33	15	42
TMR_00586	tmRNA links to Rfam database...	0.52	0.51	0.54	49	60984	52	8	34	10	48
TMR_00616	tmRNA links to Rfam database...	0.39	0.40	0.38	40	67057	69	13	51	5	59
TMR_00699	tmRNA links to Rfam database...	0.45	0.42	0.48	43	67072	52	7	39	6	59
TMR_00702	tmRNA links to Rfam database...	0.40	0.38	0.42	38	67071	58	13	39	6	62
TMR_00703	tmRNA links to Rfam database...	0.48	0.47	0.48	47	67430	56	11	40	5	52

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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 ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

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