CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CRWrnafold		CMfinder(seed)
MCC	0.589	>	0.454
Average MCC ± 95% Confidence Intervals	0.559 ± 0.071	>	0.456 ± 0.042
Sensitivity	0.596	>	0.271
Positive Predictive Value	0.584	<	0.762
Total TP	2745	>	1249
Total TN	2619987	<	2623051
Total FP	2337	>	419
Total FP CONTRA	384	>	30
Total FP INCONS	1574	>	360
Total FP COMP	379	>	29
Total FN	1858	<	3354
P-value	3.56938820447e-08

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Performance plots

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

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Performance of CRWrnafold - scored higher in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	2745
Total TN	2619987
Total FP	2337
Total FP CONTRA	384
Total FP INCONS	1574
Total FP COMP	379
Total FN	1858

Total Scores
MCC	0.589
Average MCC ± 95% Confidence Intervals	0.559 ± 0.071
Sensitivity	0.596
Positive Predictive Value	0.584
Nr of predictions	51

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2. Individual counts for CRWrnafold [ 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...	0.24	0.25	0.24	29	103617	106	20	74	12	86
CRW_00016	Intron_gpI links to Rfam database...	0.59	0.56	0.61	67	77312	55	6	36	13	53
CRW_00610	Intron_gpI links to Rfam database...	0.46	0.44	0.48	36	36240	39	7	32	0	45
CRW_00613	Intron_gpI links to Rfam database...	0.79	0.74	0.84	58	34911	19	0	11	8	20
CRW_00614	Intron_gpI links to Rfam database...	0.09	0.11	0.08	6	121691	140	26	48	66	51
CRW_00618	Intron_gpI links to Rfam database...	0.20	0.21	0.19	13	56212	77	12	43	22	48
CRW_00633	Intron_gpI links to Rfam database...	0.39	0.42	0.38	44	63429	73	15	58	0	62
CRW_00634	Intron_gpI links to Rfam database...	0.25	0.28	0.22	26	64504	92	23	67	2	68
CRW_00670	Intron_gpI links to Rfam database...	0.45	0.47	0.44	56	69999	70	9	61	0	64
CRW_00671	Intron_gpI links to Rfam database...	0.61	0.58	0.64	68	62728	44	7	32	5	49
CRW_00672	Intron_gpI links to Rfam database...	0.76	0.77	0.75	85	72276	39	6	23	10	26
CRW_00674	Intron_gpI links to Rfam database...	0.55	0.55	0.56	68	83314	58	12	42	4	56
CRW_00676	Intron_gpI links to Rfam database...	0.52	0.57	0.47	65	93390	78	24	49	5	50
CRW_00692	Intron_gpI links to Rfam database...	0.39	0.40	0.39	36	68542	75	10	47	18	54
PDB_00827	Intron_gpI links to Rfam database...	0.69	0.63	0.76	51	26961	18	0	16	2	30
RFA_00606	Telomerase-cil links to Rfam database...	0.41	0.46	0.37	18	21272	38	17	14	7	21
RFA_00620	Telomerase-cil links to Rfam database...	0.55	0.59	0.51	23	21900	40	4	18	18	16
RFA_00626	rne5 links to Rfam database...	0.64	0.63	0.65	55	56532	42	8	21	13	32
RFA_00627	rne5 links to Rfam database...	0.65	0.63	0.67	55	56871	42	6	21	15	32
RFA_00628	rne5 links to Rfam database...	0.89	0.85	0.94	73	57213	30	0	5	25	13
RFA_00630	rne5 links to Rfam database...	0.57	0.57	0.57	50	56865	51	12	26	13	37
RFA_00639	7SK links to Rfam database...	0.11	0.11	0.11	10	54524	86	13	68	5	77
RFA_00814	R2_retro_el links to Rfam database...	0.24	0.27	0.21	11	25148	48	10	31	7	30
RFA_00815	R2_retro_el links to Rfam database...	0.36	0.41	0.31	17	24477	49	6	31	12	24
RFA_00816	R2_retro_el links to Rfam database...	0.21	0.24	0.19	10	23166	50	20	24	6	31
RFA_00817	R2_retro_el links to Rfam database...	0.10	0.12	0.08	5	21883	57	17	40	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	20249	56	19	33	4	41
RFA_00819	R2_retro_el links to Rfam database...	0.44	0.44	0.44	18	27925	57	0	23	34	23
SRP_00016	Archaea_SRP links to Rfam database...	0.86	0.83	0.88	91	47792	14	0	12	2	18
SRP_00130	Archaea_SRP links to Rfam database...	0.74	0.73	0.76	71	49676	27	0	23	4	26
SRP_00142	Archaea_SRP links to Rfam database...	0.71	0.70	0.73	65	45967	28	0	24	4	28
SRP_00143	Archaea_SRP links to Rfam database...	0.81	0.80	0.83	81	49672	22	0	17	5	20
SRP_00144	Archaea_SRP links to Rfam database...	0.66	0.65	0.67	61	46574	34	1	29	4	33
SRP_00197	Archaea_SRP links to Rfam database...	0.15	0.15	0.16	15	49362	78	9	69	0	86
SRP_00198	Archaea_SRP links to Rfam database...	0.39	0.39	0.39	40	50938	63	4	58	1	63
SRP_00199	Archaea_SRP links to Rfam database...	0.70	0.70	0.70	73	50936	32	3	28	1	32
SRP_00201	Archaea_SRP links to Rfam database...	0.85	0.84	0.86	93	47787	17	5	10	2	18
SRP_00202	Archaea_SRP links to Rfam database...	0.85	0.84	0.87	98	54172	16	2	13	1	19
SRP_00203	Archaea_SRP links to Rfam database...	0.73	0.75	0.71	79	48717	40	3	29	8	26
SRP_00204	Archaea_SRP links to Rfam database...	0.71	0.71	0.71	72	49040	30	7	22	1	30
SRP_00206	Archaea_SRP links to Rfam database...	0.86	0.85	0.86	92	47788	16	5	10	1	16
SRP_00208	Archaea_SRP links to Rfam database...	0.82	0.81	0.84	82	46567	19	2	14	3	19
SRP_00255	Archaea_SRP links to Rfam database...	0.63	0.65	0.61	61	47486	41	7	32	2	33
SRP_00276	Archaea_SRP links to Rfam database...	0.85	0.84	0.86	92	50614	16	5	10	1	18
SRP_00278	Archaea_SRP links to Rfam database...	0.77	0.76	0.77	80	45952	26	5	19	2	25
SRP_00321	Archaea_SRP links to Rfam database...	0.67	0.67	0.67	72	47478	37	4	32	1	36
SRP_00322	Archaea_SRP links to Rfam database...	0.82	0.82	0.82	89	48407	20	3	17	0	20
SRP_00323	Archaea_SRP links to Rfam database...	0.94	0.93	0.95	100	47173	8	0	5	3	7
SRP_00330	Archaea_SRP links to Rfam database...	0.36	0.37	0.36	35	49989	64	4	58	2	60
SRP_00332	Archaea_SRP links to Rfam database...	0.89	0.88	0.90	93	50300	14	1	9	4	13
SRP_00339	Archaea_SRP links to Rfam database...	0.58	0.61	0.56	57	44449	46	5	40	1	37

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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 CRWrnafold - scored higher in this pairwise comparison

1. Total counts & total scores for CRWrnafold

2. Individual counts for CRWrnafold [ 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 ]