CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	UNAFold		CMfinder(seed)
MCC	0.619	>	0.454
Average MCC ± 95% Confidence Intervals	0.608 ± 0.067	>	0.456 ± 0.042
Sensitivity	0.617	>	0.271
Positive Predictive Value	0.623	<	0.762
Total TP	2840	>	1249
Total TN	2620130	<	2623051
Total FP	2112	>	419
Total FP CONTRA	352	>	30
Total FP INCONS	1368	>	360
Total FP COMP	392	>	29
Total FN	1763	<	3354
P-value	3.56938820447e-08

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Performance plots

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

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Performance of UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

Total Base Pair Counts
Total TP	2840
Total TN	2620130
Total FP	2112
Total FP CONTRA	352
Total FP INCONS	1368
Total FP COMP	392
Total FN	1763

Total Scores
MCC	0.619
Average MCC ± 95% Confidence Intervals	0.608 ± 0.067
Sensitivity	0.617
Positive Predictive Value	0.623
Nr of predictions	51

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2. Individual counts for UNAFold [ 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	0.24	0.24	28	103624	107	18	70	19	87
CRW_00016	Intron_gpI links to Rfam database...	0.62	0.57	0.67	68	77320	45	5	28	12	52
CRW_00610	Intron_gpI links to Rfam database...	0.45	0.44	0.46	36	36236	43	6	37	0	45
CRW_00613	Intron_gpI links to Rfam database...	0.63	0.58	0.68	45	34914	29	1	20	8	33
CRW_00614	Intron_gpI links to Rfam database...	0.09	0.11	0.08	6	121694	140	20	51	69	51
CRW_00618	Intron_gpI links to Rfam database...	0.18	0.20	0.17	12	56210	83	10	48	25	49
CRW_00633	Intron_gpI links to Rfam database...	0.69	0.67	0.71	71	63446	33	8	21	4	35
CRW_00634	Intron_gpI links to Rfam database...	0.33	0.34	0.33	32	64522	70	14	52	4	62
CRW_00670	Intron_gpI links to Rfam database...	0.79	0.74	0.83	89	70018	21	6	12	3	31
CRW_00671	Intron_gpI links to Rfam database...	0.65	0.62	0.68	72	62729	39	7	27	5	45
CRW_00672	Intron_gpI links to Rfam database...	0.48	0.49	0.47	54	72275	65	19	42	4	57
CRW_00674	Intron_gpI links to Rfam database...	0.58	0.56	0.62	69	83324	45	7	36	2	55
CRW_00676	Intron_gpI links to Rfam database...	0.54	0.55	0.53	63	93410	69	15	40	14	52
CRW_00692	Intron_gpI links to Rfam database...	0.20	0.21	0.19	19	68537	84	24	55	5	71
PDB_00827	Intron_gpI links to Rfam database...	0.58	0.52	0.66	42	26964	23	1	21	1	39
RFA_00606	Telomerase-cil links to Rfam database...	0.67	0.67	0.68	26	21283	25	7	5	13	13
RFA_00620	Telomerase-cil links to Rfam database...	0.67	0.64	0.69	25	21909	24	3	8	13	14
RFA_00626	rne5 links to Rfam database...	0.87	0.84	0.91	73	56536	32	2	5	25	14
RFA_00627	rne5 links to Rfam database...	0.70	0.67	0.74	58	56875	36	4	16	16	29
RFA_00628	rne5 links to Rfam database...	0.86	0.83	0.89	71	57211	31	1	8	22	15
RFA_00630	rne5 links to Rfam database...	0.59	0.59	0.59	51	56866	48	8	28	12	36
RFA_00639	7SK links to Rfam database...	0.17	0.18	0.16	16	54518	83	18	63	2	71
RFA_00814	R2_retro_el links to Rfam database...	0.77	0.78	0.76	32	25158	23	4	6	13	9
RFA_00815	R2_retro_el links to Rfam database...	0.56	0.61	0.51	25	24482	36	8	16	12	16
RFA_00816	R2_retro_el links to Rfam database...	0.60	0.66	0.55	27	23171	30	13	9	8	14
RFA_00817	R2_retro_el links to Rfam database...	0.10	0.12	0.08	5	21882	58	18	40	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.19	0.22	0.17	9	20247	46	19	26	1	32
RFA_00819	R2_retro_el links to Rfam database...	0.96	0.95	0.98	39	27926	28	0	1	27	2
SRP_00016	Archaea_SRP links to Rfam database...	0.91	0.87	0.94	95	47794	8	0	6	2	14
SRP_00130	Archaea_SRP links to Rfam database...	0.27	0.27	0.27	26	49675	69	10	59	0	71
SRP_00142	Archaea_SRP links to Rfam database...	0.59	0.60	0.58	56	45960	42	5	35	2	37
SRP_00143	Archaea_SRP links to Rfam database...	0.85	0.84	0.86	85	49671	19	1	13	5	16
SRP_00144	Archaea_SRP links to Rfam database...	0.74	0.73	0.75	69	46573	30	1	22	7	25
SRP_00197	Archaea_SRP links to Rfam database...	0.44	0.43	0.45	43	49360	53	4	48	1	58
SRP_00198	Archaea_SRP links to Rfam database...	0.34	0.34	0.35	35	50940	66	4	61	1	68
SRP_00199	Archaea_SRP links to Rfam database...	0.65	0.65	0.66	68	50937	36	3	32	1	37
SRP_00201	Archaea_SRP links to Rfam database...	0.94	0.92	0.95	102	47788	7	0	5	2	9
SRP_00202	Archaea_SRP links to Rfam database...	0.97	0.95	0.98	111	54172	4	0	2	2	6
SRP_00203	Archaea_SRP links to Rfam database...	0.73	0.75	0.72	79	48718	37	3	28	6	26
SRP_00204	Archaea_SRP links to Rfam database...	0.60	0.61	0.60	62	49038	42	7	34	1	40
SRP_00206	Archaea_SRP links to Rfam database...	0.82	0.81	0.83	87	47790	19	5	13	1	21
SRP_00208	Archaea_SRP links to Rfam database...	0.85	0.81	0.88	82	46572	14	1	10	3	19
SRP_00255	Archaea_SRP links to Rfam database...	0.60	0.62	0.59	58	47487	46	3	38	5	36
SRP_00276	Archaea_SRP links to Rfam database...	0.87	0.85	0.88	94	50614	14	5	8	1	16
SRP_00278	Archaea_SRP links to Rfam database...	0.77	0.76	0.78	80	45954	23	5	17	1	25
SRP_00321	Archaea_SRP links to Rfam database...	0.64	0.64	0.65	69	47480	38	7	30	1	39
SRP_00322	Archaea_SRP links to Rfam database...	0.61	0.61	0.60	67	48405	45	6	38	1	42
SRP_00323	Archaea_SRP links to Rfam database...	0.93	0.92	0.94	98	47174	8	0	6	2	9
SRP_00330	Archaea_SRP links to Rfam database...	0.63	0.64	0.63	61	49989	40	4	32	4	34
SRP_00332	Archaea_SRP links to Rfam database...	0.84	0.85	0.83	90	50295	19	6	12	1	16
SRP_00339	Archaea_SRP links to Rfam database...	0.64	0.64	0.64	60	44457	37	6	28	3	34

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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 UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

2. Individual counts for UNAFold [ 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 ]