CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Fold		CMfinder(seed)
MCC	0.594	>	0.454
Average MCC ± 95% Confidence Intervals	0.584 ± 0.059	>	0.456 ± 0.042
Sensitivity	0.604	>	0.271
Positive Predictive Value	0.586	<	0.762
Total TP	2780	>	1249
Total TN	2619950	<	2623051
Total FP	2420	>	419
Total FP CONTRA	352	>	30
Total FP INCONS	1608	>	360
Total FP COMP	460	>	29
Total FN	1823	<	3354
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Fold and CMfinder(seed). 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 Fold and CMfinder(seed)).
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 Fold and CMfinder(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Fold and CMfinder(seed). 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 Fold and CMfinder(seed)).

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Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	2780
Total TN	2619950
Total FP	2420
Total FP CONTRA	352
Total FP INCONS	1608
Total FP COMP	460
Total FN	1823

Total Scores
MCC	0.594
Average MCC ± 95% Confidence Intervals	0.584 ± 0.059
Sensitivity	0.604
Positive Predictive Value	0.586
Nr of predictions	51

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00013	Intron_gpI links to Rfam database...	0.21	0.21	0.21	24	103627	115	11	78	26	91
CRW_00016	Intron_gpI links to Rfam database...	0.79	0.75	0.83	90	77313	31	5	13	13	30
CRW_00610	Intron_gpI links to Rfam database...	0.43	0.43	0.42	35	36232	49	9	39	1	46
CRW_00613	Intron_gpI links to Rfam database...	0.89	0.85	0.93	66	34909	13	0	5	8	12
CRW_00614	Intron_gpI links to Rfam database...	0.13	0.16	0.11	9	121688	143	18	56	69	48
CRW_00618	Intron_gpI links to Rfam database...	0.19	0.20	0.18	12	56212	81	8	48	25	49
CRW_00633	Intron_gpI links to Rfam database...	0.44	0.43	0.44	46	63441	61	13	46	2	60
CRW_00634	Intron_gpI links to Rfam database...	0.28	0.30	0.26	28	64513	83	12	67	4	66
CRW_00670	Intron_gpI links to Rfam database...	0.54	0.55	0.54	66	70002	59	12	45	2	54
CRW_00671	Intron_gpI links to Rfam database...	0.71	0.68	0.74	79	62728	34	1	27	6	38
CRW_00672	Intron_gpI links to Rfam database...	0.75	0.77	0.74	85	72275	40	6	24	10	26
CRW_00674	Intron_gpI links to Rfam database...	0.66	0.67	0.66	83	83310	52	9	34	9	41
CRW_00676	Intron_gpI links to Rfam database...	0.55	0.57	0.54	66	93405	75	12	45	18	49
CRW_00692	Intron_gpI links to Rfam database...	0.23	0.24	0.21	22	68530	90	27	56	7	68
PDB_00827	Intron_gpI links to Rfam database...	0.65	0.59	0.72	48	26961	21	0	19	2	33
RFA_00606	Telomerase-cil links to Rfam database...	0.68	0.67	0.70	26	21284	27	7	4	16	13
RFA_00620	Telomerase-cil links to Rfam database...	0.47	0.49	0.45	19	21903	36	7	16	13	20
RFA_00626	rne5 links to Rfam database...	0.86	0.82	0.90	71	56537	35	2	6	27	16
RFA_00627	rne5 links to Rfam database...	0.68	0.67	0.69	58	56869	42	7	19	16	29
RFA_00628	rne5 links to Rfam database...	0.87	0.84	0.90	72	57211	30	0	8	22	14
RFA_00630	rne5 links to Rfam database...	0.62	0.63	0.61	55	56863	52	9	26	17	32
RFA_00639	7SK links to Rfam database...	0.47	0.51	0.44	44	54516	64	15	40	9	43
RFA_00814	R2_retro_el links to Rfam database...	0.22	0.24	0.19	10	25148	51	11	31	9	31
RFA_00815	R2_retro_el links to Rfam database...	0.57	0.61	0.54	25	24485	37	4	17	16	16
RFA_00816	R2_retro_el links to Rfam database...	0.61	0.66	0.56	27	23172	33	13	8	12	14
RFA_00817	R2_retro_el links to Rfam database...	0.35	0.41	0.30	17	21889	43	11	28	4	24
RFA_00818	R2_retro_el links to Rfam database...	0.46	0.54	0.40	22	20246	38	13	20	5	19
RFA_00819	R2_retro_el links to Rfam database...	0.83	0.80	0.85	33	27927	41	0	6	35	8
SRP_00016	Archaea_SRP links to Rfam database...	0.78	0.78	0.77	85	47785	26	4	21	1	24
SRP_00130	Archaea_SRP links to Rfam database...	0.67	0.68	0.65	66	49669	39	4	31	4	31
SRP_00142	Archaea_SRP links to Rfam database...	0.56	0.58	0.54	54	45956	48	5	41	2	39
SRP_00143	Archaea_SRP links to Rfam database...	0.36	0.38	0.35	38	49660	74	7	65	2	63
SRP_00144	Archaea_SRP links to Rfam database...	0.41	0.43	0.40	40	46564	66	9	52	5	54
SRP_00197	Archaea_SRP links to Rfam database...	0.34	0.33	0.35	33	49360	62	5	57	0	68
SRP_00198	Archaea_SRP links to Rfam database...	0.21	0.21	0.21	22	50936	82	8	74	0	81
SRP_00199	Archaea_SRP links to Rfam database...	0.62	0.62	0.61	65	50934	43	3	38	2	40
SRP_00201	Archaea_SRP links to Rfam database...	0.77	0.77	0.78	85	47786	26	1	23	2	26
SRP_00202	Archaea_SRP links to Rfam database...	0.89	0.89	0.89	104	54168	15	2	11	2	13
SRP_00203	Archaea_SRP links to Rfam database...	0.71	0.72	0.69	76	48718	42	1	33	8	29
SRP_00204	Archaea_SRP links to Rfam database...	0.66	0.67	0.65	68	49037	37	7	29	1	34
SRP_00206	Archaea_SRP links to Rfam database...	0.84	0.83	0.84	90	47788	18	6	11	1	18
SRP_00208	Archaea_SRP links to Rfam database...	0.64	0.63	0.65	64	46566	37	6	29	2	37
SRP_00255	Archaea_SRP links to Rfam database...	0.54	0.55	0.52	52	47486	53	3	45	5	42
SRP_00276	Archaea_SRP links to Rfam database...	0.86	0.85	0.86	94	50612	16	5	10	1	16
SRP_00278	Archaea_SRP links to Rfam database...	0.66	0.67	0.66	70	45950	39	6	30	3	35
SRP_00321	Archaea_SRP links to Rfam database...	0.56	0.57	0.54	62	47471	54	11	42	1	46
SRP_00322	Archaea_SRP links to Rfam database...	0.77	0.77	0.76	84	48406	28	0	26	2	25
SRP_00323	Archaea_SRP links to Rfam database...	0.81	0.80	0.81	86	47172	23	0	20	3	21
SRP_00330	Archaea_SRP links to Rfam database...	0.69	0.71	0.67	67	49986	37	4	29	4	28
SRP_00332	Archaea_SRP links to Rfam database...	0.67	0.69	0.66	73	50292	39	8	30	1	33
SRP_00339	Archaea_SRP links to Rfam database...	0.66	0.68	0.65	64	44452	40	5	30	5	30

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Performance of CMfinder(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	1249
Total TN	2623051
Total FP	419
Total FP CONTRA	30
Total FP INCONS	360
Total FP COMP	29
Total FN	3354

Total Scores
MCC	0.454
Average MCC ± 95% Confidence Intervals	0.456 ± 0.042
Sensitivity	0.271
Positive Predictive Value	0.762
Nr of predictions	51

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00013	Intron_gpI links to Rfam database...	0.37	0.14	1.00	16	103724	0	0	0	0	99
CRW_00016	Intron_gpI links to Rfam database...	0.36	0.14	0.89	17	77402	2	0	2	0	103
CRW_00610	Intron_gpI links to Rfam database...	0.49	0.31	0.78	25	36283	7	1	6	0	56
CRW_00613	Intron_gpI links to Rfam database...	0.54	0.33	0.87	26	34950	4	0	4	0	52
CRW_00614	Intron_gpI links to Rfam database...	0.46	0.25	0.88	14	121755	9	0	2	7	43
CRW_00618	Intron_gpI links to Rfam database...	0.36	0.13	1.00	8	56272	0	0	0	0	53
CRW_00633	Intron_gpI links to Rfam database...	0.32	0.12	0.81	13	63530	3	1	2	0	93
CRW_00634	Intron_gpI links to Rfam database...	0.40	0.17	0.94	16	64603	1	0	1	0	78
CRW_00670	Intron_gpI links to Rfam database...	0.32	0.18	0.55	22	70085	18	0	18	0	98
CRW_00671	Intron_gpI links to Rfam database...	0.20	0.09	0.41	11	62808	16	0	16	0	106
CRW_00672	Intron_gpI links to Rfam database...	0.38	0.15	0.94	17	72372	1	0	1	0	94
CRW_00674	Intron_gpI links to Rfam database...	0.40	0.17	0.95	21	83414	1	0	1	0	103
CRW_00676	Intron_gpI links to Rfam database...	0.12	0.04	0.33	5	93513	10	1	9	0	110
CRW_00692	Intron_gpI links to Rfam database...	0.41	0.17	1.00	15	68620	0	0	0	0	75
PDB_00827	Intron_gpI links to Rfam database...	0.25	0.10	0.62	8	27015	5	0	5	0	73
RFA_00606	Telomerase-cil links to Rfam database...	0.34	0.21	0.57	8	21307	8	2	4	2	31
RFA_00620	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	21939	6	0	6	0	39
RFA_00626	rne5 links to Rfam database...	0.44	0.32	0.60	28	56569	22	2	17	3	59
RFA_00627	rne5 links to Rfam database...	0.53	0.39	0.72	34	56906	15	3	10	2	53
RFA_00628	rne5 links to Rfam database...	0.58	0.43	0.77	37	57243	14	3	8	3	49
RFA_00630	rne5 links to Rfam database...	0.45	0.32	0.64	28	56909	17	3	13	1	59
RFA_00639	7SK links to Rfam database...	0.00	0.00	0.00	0	54575	44	6	34	4	87
RFA_00814	R2_retro_el links to Rfam database...	0.68	0.51	0.91	21	25177	2	0	2	0	20
RFA_00815	R2_retro_el links to Rfam database...	0.68	0.51	0.91	21	24508	2	0	2	0	20
RFA_00816	R2_retro_el links to Rfam database...	0.68	0.51	0.91	21	23197	2	0	2	0	20
RFA_00817	R2_retro_el links to Rfam database...	0.68	0.56	0.82	23	21917	5	0	5	0	18
RFA_00818	R2_retro_el links to Rfam database...	0.60	0.49	0.74	20	20274	8	1	6	1	21
RFA_00819	R2_retro_el links to Rfam database...	0.62	0.51	0.75	21	27938	7	0	7	0	20
SRP_00016	Archaea_SRP links to Rfam database...	0.54	0.35	0.83	38	47849	8	0	8	0	71
SRP_00130	Archaea_SRP links to Rfam database...	0.50	0.32	0.78	31	49730	10	1	8	1	66
SRP_00142	Archaea_SRP links to Rfam database...	0.46	0.37	0.58	34	45997	26	1	24	1	59
SRP_00143	Archaea_SRP links to Rfam database...	0.50	0.30	0.86	30	49735	5	0	5	0	71
SRP_00144	Archaea_SRP links to Rfam database...	0.54	0.37	0.80	35	46621	11	0	9	2	59
SRP_00197	Archaea_SRP links to Rfam database...	0.46	0.26	0.84	26	49424	5	0	5	0	75
SRP_00198	Archaea_SRP links to Rfam database...	0.56	0.37	0.84	38	50995	7	0	7	0	65
SRP_00199	Archaea_SRP links to Rfam database...	0.54	0.35	0.82	37	50995	8	0	8	0	68
SRP_00201	Archaea_SRP links to Rfam database...	0.54	0.35	0.83	39	47848	8	0	8	0	72
SRP_00202	Archaea_SRP links to Rfam database...	0.43	0.21	0.86	25	54256	4	0	4	0	92
SRP_00203	Archaea_SRP links to Rfam database...	0.51	0.34	0.77	36	48781	12	0	11	1	69
SRP_00204	Archaea_SRP links to Rfam database...	0.52	0.34	0.80	35	49097	9	1	8	0	67
SRP_00206	Archaea_SRP links to Rfam database...	0.55	0.36	0.83	39	47848	8	0	8	0	69
SRP_00208	Archaea_SRP links to Rfam database...	0.52	0.33	0.83	33	46625	7	1	6	0	68
SRP_00255	Archaea_SRP links to Rfam database...	0.49	0.27	0.89	25	47558	3	0	3	0	69
SRP_00276	Archaea_SRP links to Rfam database...	0.51	0.33	0.80	36	50676	9	0	9	0	74
SRP_00278	Archaea_SRP links to Rfam database...	0.52	0.33	0.81	35	46013	8	0	8	0	70
SRP_00321	Archaea_SRP links to Rfam database...	0.42	0.21	0.82	23	47558	5	1	4	0	85
SRP_00322	Archaea_SRP links to Rfam database...	0.52	0.33	0.82	36	48472	8	0	8	0	73
SRP_00323	Archaea_SRP links to Rfam database...	0.54	0.34	0.88	36	47237	5	0	5	0	71
SRP_00330	Archaea_SRP links to Rfam database...	0.44	0.23	0.85	22	50060	5	0	4	1	73
SRP_00332	Archaea_SRP links to Rfam database...	0.44	0.25	0.75	27	50367	9	0	9	0	79
SRP_00339	Archaea_SRP links to Rfam database...	0.56	0.39	0.79	37	44504	10	2	8	0	57

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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 Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

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

Performance of CMfinder(seed) - scored lower in this pairwise comparison

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

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