CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Contrafold		CMfinder(seed)
MCC	0.677	>	0.454
Average MCC ± 95% Confidence Intervals	0.660 ± 0.055	>	0.456 ± 0.042
Sensitivity	0.673	>	0.271
Positive Predictive Value	0.683	<	0.762
Total TP	3098	>	1249
Total TN	2620153	<	2623051
Total FP	1907	>	419
Total FP CONTRA	247	>	30
Total FP INCONS	1192	>	360
Total FP COMP	468	>	29
Total FN	1505	<	3354
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	3098
Total TN	2620153
Total FP	1907
Total FP CONTRA	247
Total FP INCONS	1192
Total FP COMP	468
Total FN	1505

Total Scores
MCC	0.677
Average MCC ± 95% Confidence Intervals	0.660 ± 0.055
Sensitivity	0.673
Positive Predictive Value	0.683
Nr of predictions	51

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2. Individual counts for Contrafold [ 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...	0.43	0.39	0.47	45	103644	80	11	40	29	70
CRW_00016	Intron_gpI links to Rfam database...	0.73	0.68	0.79	81	77319	37	0	21	16	39
CRW_00610	Intron_gpI links to Rfam database...	0.50	0.49	0.51	40	36237	41	9	29	3	41
CRW_00613	Intron_gpI links to Rfam database...	0.79	0.77	0.81	60	34906	22	1	13	8	18
CRW_00614	Intron_gpI links to Rfam database...	0.24	0.25	0.23	14	121709	121	7	41	73	43
CRW_00618	Intron_gpI links to Rfam database...	0.20	0.21	0.19	13	56213	75	8	46	21	48
CRW_00633	Intron_gpI links to Rfam database...	0.58	0.55	0.62	58	63453	37	8	27	2	48
CRW_00634	Intron_gpI links to Rfam database...	0.58	0.59	0.57	55	64524	43	12	29	2	39
CRW_00670	Intron_gpI links to Rfam database...	0.76	0.71	0.83	85	70022	19	0	18	1	35
CRW_00671	Intron_gpI links to Rfam database...	0.73	0.70	0.77	82	62728	31	1	24	6	35
CRW_00672	Intron_gpI links to Rfam database...	0.53	0.52	0.55	58	72284	55	8	40	7	53
CRW_00674	Intron_gpI links to Rfam database...	0.70	0.66	0.74	82	83325	34	5	24	5	42
CRW_00676	Intron_gpI links to Rfam database...	0.42	0.44	0.40	51	93400	81	20	57	4	64
CRW_00692	Intron_gpI links to Rfam database...	0.45	0.44	0.47	40	68549	53	16	30	7	50
PDB_00827	Intron_gpI links to Rfam database...	0.77	0.65	0.90	53	26969	8	0	6	2	28
RFA_00606	Telomerase-cil links to Rfam database...	0.53	0.51	0.54	20	21284	25	10	7	8	19
RFA_00620	Telomerase-cil links to Rfam database...	0.71	0.64	0.78	25	21913	29	0	7	22	14
RFA_00626	rne5 links to Rfam database...	0.91	0.87	0.94	76	56535	26	1	4	21	11
RFA_00627	rne5 links to Rfam database...	0.86	0.83	0.89	72	56872	28	0	9	19	15
RFA_00628	rne5 links to Rfam database...	0.91	0.88	0.94	76	57210	25	0	5	20	10
RFA_00630	rne5 links to Rfam database...	0.77	0.77	0.77	67	56866	34	6	14	14	20
RFA_00639	7SK links to Rfam database...	0.60	0.59	0.61	51	54532	47	5	27	15	36
RFA_00814	R2_retro_el links to Rfam database...	0.79	0.78	0.80	32	25160	19	1	7	11	9
RFA_00815	R2_retro_el links to Rfam database...	0.59	0.61	0.57	25	24487	35	2	17	16	16
RFA_00816	R2_retro_el links to Rfam database...	0.72	0.73	0.71	30	23178	20	8	4	8	11
RFA_00817	R2_retro_el links to Rfam database...	0.11	0.12	0.10	5	21893	47	12	35	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.57	0.61	0.53	25	20254	32	11	11	10	16
RFA_00819	R2_retro_el links to Rfam database...	0.46	0.46	0.45	19	27924	47	3	20	24	22
SRP_00016	Archaea_SRP links to Rfam database...	0.93	0.93	0.94	101	47787	10	1	6	3	8
SRP_00130	Archaea_SRP links to Rfam database...	0.69	0.70	0.67	68	49669	38	4	29	5	29
SRP_00142	Archaea_SRP links to Rfam database...	0.54	0.55	0.53	51	45959	48	5	41	2	42
SRP_00143	Archaea_SRP links to Rfam database...	0.74	0.75	0.74	76	49667	35	1	26	8	25
SRP_00144	Archaea_SRP links to Rfam database...	0.72	0.71	0.72	67	46572	34	2	24	8	27
SRP_00197	Archaea_SRP links to Rfam database...	0.24	0.22	0.26	22	49370	63	10	53	0	79
SRP_00198	Archaea_SRP links to Rfam database...	0.48	0.49	0.48	50	50936	55	2	52	1	53
SRP_00199	Archaea_SRP links to Rfam database...	0.61	0.60	0.62	63	50939	42	3	35	4	42
SRP_00201	Archaea_SRP links to Rfam database...	0.85	0.85	0.85	94	47784	20	5	12	3	17
SRP_00202	Archaea_SRP links to Rfam database...	0.89	0.89	0.89	104	54168	16	1	12	3	13
SRP_00203	Archaea_SRP links to Rfam database...	0.73	0.74	0.71	78	48718	42	2	30	10	27
SRP_00204	Archaea_SRP links to Rfam database...	0.73	0.74	0.72	75	49037	31	6	23	2	27
SRP_00206	Archaea_SRP links to Rfam database...	0.85	0.86	0.84	93	47784	21	6	12	3	15
SRP_00208	Archaea_SRP links to Rfam database...	0.85	0.86	0.84	87	46561	23	3	14	6	14
SRP_00255	Archaea_SRP links to Rfam database...	0.81	0.82	0.79	77	47489	27	2	18	7	17
SRP_00276	Archaea_SRP links to Rfam database...	0.87	0.88	0.87	97	50609	18	5	10	3	13
SRP_00278	Archaea_SRP links to Rfam database...	0.73	0.74	0.72	78	45947	33	4	27	2	27
SRP_00321	Archaea_SRP links to Rfam database...	0.68	0.70	0.67	76	47472	41	3	35	3	32
SRP_00322	Archaea_SRP links to Rfam database...	0.89	0.90	0.88	98	48404	17	1	13	3	11
SRP_00323	Archaea_SRP links to Rfam database...	0.94	0.94	0.94	101	47171	9	0	6	3	6
SRP_00330	Archaea_SRP links to Rfam database...	0.61	0.65	0.57	62	49978	52	4	42	6	33
SRP_00332	Archaea_SRP links to Rfam database...	0.70	0.72	0.68	76	50291	39	8	28	3	30
SRP_00339	Archaea_SRP links to Rfam database...	0.66	0.68	0.64	64	44451	42	4	32	6	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 Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

2. Individual counts for Contrafold [ 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 ]