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		Carnac(seed)
MCC	0.599	>	0.150
Average MCC ± 95% Confidence Intervals	0.587 ± 0.031	>	0.057 ± 0.030
Sensitivity	0.601	>	0.028
Positive Predictive Value	0.599	<	0.809
Total TP	8285	>	385
Total TN	8658964	<	8672323
Total FP	7016	>	134
Total FP CONTRA	978	>	4
Total FP INCONS	4572	>	87
Total FP COMP	1466	>	43
Total FN	5508	<	13408
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Contrafold and Carnac(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 Carnac(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 Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Contrafold and Carnac(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 Carnac(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	8285
Total TN	8658964
Total FP	7016
Total FP CONTRA	978
Total FP INCONS	4572
Total FP COMP	1466
Total FN	5508

Total Scores
MCC	0.599
Average MCC ± 95% Confidence Intervals	0.587 ± 0.031
Sensitivity	0.601
Positive Predictive Value	0.599
Nr of predictions	145

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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
ASE_00001	RNaseP_arch links to Rfam database...	0.80	0.77	0.83	58	34121	21	3	9	9	17
ASE_00002	RNaseP_arch links to Rfam database...	0.59	0.56	0.61	41	35444	30	2	24	4	32
ASE_00009	RNaseP_arch links to Rfam database...	0.66	0.64	0.68	43	26043	23	1	19	3	24
ASE_00014	RNaseP_arch links to Rfam database...	0.53	0.53	0.53	56	54179	54	6	44	4	50
ASE_00116	RNaseP_arch links to Rfam database...	0.46	0.42	0.50	28	31570	31	0	28	3	38
ASE_00120	RNaseP_arch links to Rfam database...	0.60	0.57	0.64	54	46886	31	6	25	0	40
ASE_00121	RNaseP_arch links to Rfam database...	0.28	0.27	0.29	25	45063	64	6	56	2	67
ASE_00145	RNaseP_arch links to Rfam database...	0.60	0.59	0.60	66	70015	50	7	37	6	45
ASE_00148	RNaseP_arch links to Rfam database...	0.79	0.78	0.81	120	112426	34	5	24	5	34
ASE_00154	RNaseP_arch links to Rfam database...	0.74	0.72	0.76	77	65240	31	2	22	7	30
ASE_00155	RNaseP_arch links to Rfam database...	0.60	0.58	0.61	83	93392	56	4	49	3	59
ASE_00187	RNaseP_arch links to Rfam database...	0.38	0.37	0.40	42	68531	68	5	57	6	73
ASE_00191	RNaseP_arch links to Rfam database...	0.70	0.67	0.73	41	29590	20	1	14	5	20
ASE_00196	RNaseP_arch links to Rfam database...	0.75	0.76	0.74	57	31549	26	2	18	6	18
ASE_00205	RNaseP_arch links to Rfam database...	0.45	0.46	0.45	41	45964	60	7	44	9	49
ASE_00209	RNaseP_arch links to Rfam database...	0.56	0.51	0.61	45	42997	31	3	26	2	43
ASE_00210	RNaseP_arch links to Rfam database...	0.58	0.60	0.57	39	27192	31	7	23	1	26
ASE_00213	RNaseP_arch links to Rfam database...	0.58	0.58	0.58	38	27196	30	5	22	3	28
ASE_00222	RNaseP_arch links to Rfam database...	0.72	0.71	0.74	111	111950	46	7	33	6	46
ASE_00346	RNaseP_arch links to Rfam database...	0.34	0.34	0.35	33	48111	67	4	57	6	64
ASE_00359	RNaseP_arch links to Rfam database...	0.49	0.48	0.51	38	42703	44	3	34	7	42
ASE_00360	RNaseP_arch links to Rfam database...	0.31	0.31	0.32	20	29341	43	8	34	1	45
ASE_00417	RNaseP_arch links to Rfam database...	0.47	0.47	0.47	47	54516	55	2	50	3	53
ASE_00418	RNaseP_arch links to Rfam database...	0.06	0.07	0.07	5	38706	72	5	65	2	70
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_00619	Intron_gpI links to Rfam database...	0.45	0.40	0.52	29	164969	110	5	22	83	44
CRW_00620	Intron_gpI links to Rfam database...	0.18	0.22	0.15	14	150884	136	23	54	59	49
CRW_00621	Intron_gpI links to Rfam database...	0.37	0.35	0.38	25	153116	137	6	34	97	46
CRW_00623	Intron_gpI links to Rfam database...	0.25	0.20	0.31	17	129740	100	5	33	62	66
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_00597	Telomerase-vert links to Rfam database...	0.60	0.61	0.59	67	97789	69	16	31	22	42
RFA_00598	Telomerase-vert links to Rfam database...	0.47	0.47	0.48	47	84569	79	6	44	29	54
RFA_00599	Telomerase-vert links to Rfam database...	0.71	0.73	0.70	81	101359	59	10	25	24	30
RFA_00600	Telomerase-vert links to Rfam database...	0.67	0.72	0.62	72	120178	86	21	24	41	28
RFA_00601	Telomerase-vert links to Rfam database...	0.33	0.36	0.30	41	99097	108	37	60	11	73
RFA_00602	Telomerase-vert links to Rfam database...	0.63	0.67	0.58	78	101341	68	25	31	12	38
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_00621	RNase_MRP links to Rfam database...	0.51	0.51	0.51	39	46284	58	2	35	21	37
RFA_00623	RNase_MRP links to Rfam database...	0.61	0.60	0.61	47	43879	46	1	29	16	31
RFA_00624	RNase_MRP links to Rfam database...	0.44	0.48	0.40	29	30063	49	9	34	6	32
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_00805	RNAIII links to Rfam database...	0.83	0.74	0.93	111	133266	19	1	8	10	39
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
RFA_00820	bicoid_3 links to Rfam database...	0.95	0.94	0.95	151	151366	28	0	8	20	9
RFA_00830	bicoid_3 links to Rfam database...	0.57	0.52	0.62	80	152499	100	2	47	51	74
SRP_00009	Plant_SRP links to Rfam database...	0.54	0.55	0.53	56	46560	54	8	41	5	46
SRP_00011	Plant_SRP links to Rfam database...	0.38	0.38	0.39	39	46260	62	5	56	1	65
SRP_00012	Plant_SRP links to Rfam database...	0.68	0.67	0.69	68	46261	32	7	24	1	33
SRP_00015	Plant_SRP links to Rfam database...	0.78	0.77	0.80	76	46265	26	2	17	7	23
SRP_00016	Archaea_SRP links to Rfam database...	0.93	0.93	0.94	101	47787	10	1	6	3	8
SRP_00018	Fungi_SRP links to Rfam database...	0.62	0.64	0.60	52	38417	44	7	27	10	29
SRP_00019	Fungi_SRP links to Rfam database...	0.38	0.35	0.41	32	35967	53	6	41	6	59
SRP_00069	Fungi_SRP links to Rfam database...	0.59	0.58	0.61	49	34373	33	2	29	2	36
SRP_00070	Fungi_SRP links to Rfam database...	0.35	0.39	0.31	47	126604	116	33	72	11	74
SRP_00073	Fungi_SRP links to Rfam database...	0.62	0.63	0.61	45	38986	46	6	23	17	26
SRP_00079	Plant_SRP links to Rfam database...	0.62	0.63	0.63	55	41817	43	3	30	10	33
SRP_00085	Plant_SRP links to Rfam database...	0.64	0.62	0.65	63	45354	38	5	29	4	38
SRP_00087	Fungi_SRP links to Rfam database...	0.19	0.22	0.16	13	37321	74	21	46	7	45
SRP_00091	Fungi_SRP links to Rfam database...	0.70	0.73	0.68	69	52874	39	4	28	7	26
SRP_00099	Plant_SRP links to Rfam database...	0.62	0.62	0.62	59	44755	37	7	29	1	36
SRP_00104	Fungi_SRP links to Rfam database...	0.33	0.36	0.30	25	34370	61	9	49	3	44
SRP_00124	Metazoa_SRP links to Rfam database...	0.63	0.62	0.63	53	37044	38	3	28	7	32
SRP_00127	Fungi_SRP links to Rfam database...	0.69	0.71	0.67	84	72264	48	10	32	6	35
SRP_00130	Archaea_SRP links to Rfam database...	0.69	0.70	0.67	68	49669	38	4	29	5	29
SRP_00136	Fungi_SRP links to Rfam database...	0.40	0.45	0.35	32	44162	68	15	44	9	39
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_00148	Fungi_SRP links to Rfam database...	0.47	0.49	0.46	43	49992	62	4	47	11	44
SRP_00152	Plant_SRP links to Rfam database...	0.52	0.51	0.52	53	45651	49	10	39	0	50
SRP_00153	Plant_SRP links to Rfam database...	0.74	0.75	0.73	80	46862	31	7	22	2	27
SRP_00157	Fungi_SRP links to Rfam database...	0.37	0.42	0.33	30	44162	70	15	46	9	42
SRP_00158	Fungi_SRP links to Rfam database...	0.37	0.43	0.32	50	124095	119	41	65	13	65
SRP_00160	Fungi_SRP links to Rfam database...	0.38	0.37	0.40	48	86199	73	5	68	0	82
SRP_00175	Fungi_SRP links to Rfam database...	0.33	0.33	0.34	28	44468	60	9	46	5	56
SRP_00178	Plant_SRP links to Rfam database...	0.77	0.76	0.77	78	45652	26	7	16	3	24
SRP_00179	Plant_SRP links to Rfam database...	0.80	0.79	0.81	83	45954	23	5	14	4	22
SRP_00181	Plant_SRP links to Rfam database...	0.53	0.48	0.58	49	45972	36	5	30	1	53
SRP_00182	Plant_SRP links to Rfam database...	0.58	0.58	0.58	59	45955	45	10	32	3	42
SRP_00184	Plant_SRP links to Rfam database...	0.65	0.64	0.67	64	45960	37	6	26	5	36
SRP_00188	Plant_SRP links to Rfam database...	0.21	0.22	0.21	17	31045	63	8	55	0	62
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_00230	Fungi_SRP links to Rfam database...	0.74	0.76	0.73	68	39528	31	3	22	6	22
SRP_00239	Plant_SRP links to Rfam database...	0.27	0.29	0.26	27	50300	76	14	62	0	66
SRP_00240	Plant_SRP links to Rfam database...	0.79	0.80	0.77	82	48099	32	7	17	8	20
SRP_00241	Plant_SRP links to Rfam database...	0.51	0.55	0.47	45	45961	53	14	36	3	37
SRP_00252	Metazoa_SRP links to Rfam database...	0.54	0.56	0.52	50	49044	53	7	40	6	39
SRP_00253	Metazoa_SRP links to Rfam database...	0.47	0.49	0.44	44	49356	61	9	46	6	46
SRP_00254	Fungi_SRP links to Rfam database...	0.40	0.44	0.36	27	32311	58	11	36	11	34
SRP_00255	Archaea_SRP links to Rfam database...	0.81	0.82	0.79	77	47489	27	2	18	7	17
SRP_00257	Metazoa_SRP links to Rfam database...	0.86	0.85	0.88	92	50935	22	0	13	9	16
SRP_00260	Metazoa_SRP links to Rfam database...	0.71	0.74	0.69	74	47787	37	6	28	3	26
SRP_00265	Fungi_SRP links to Rfam database...	0.65	0.67	0.63	49	41250	42	8	21	13	24
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_00286	Fungi_SRP links to Rfam database...	0.71	0.71	0.72	123	136856	58	3	44	11	51
SRP_00287	Fungi_SRP links to Rfam database...	0.49	0.50	0.48	81	141609	96	17	71	8	81
SRP_00290	Fungi_SRP links to Rfam database...	0.66	0.67	0.65	91	100435	66	4	46	16	44
SRP_00292	Fungi_SRP links to Rfam database...	0.44	0.42	0.46	73	137391	93	4	82	7	100
SRP_00294	Fungi_SRP links to Rfam database...	0.65	0.62	0.68	104	129132	54	5	45	4	63
SRP_00301	Fungi_SRP links to Rfam database...	0.62	0.58	0.66	50	32564	30	2	24	4	36
SRP_00302	Fungi_SRP links to Rfam database...	0.35	0.37	0.33	30	41525	70	7	54	9	51
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.66	0.68	0.64	60	36221	37	6	28	3	28
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_00328	Metazoa_SRP links to Rfam database...	0.60	0.62	0.58	53	39530	41	10	28	3	32
SRP_00329	Metazoa_SRP links to Rfam database...	0.59	0.61	0.58	52	39813	43	6	32	5	33
SRP_00330	Archaea_SRP links to Rfam database...	0.61	0.65	0.57	62	49978	52	4	42	6	33
SRP_00331	Metazoa_SRP links to Rfam database...	0.52	0.54	0.50	47	37581	50	10	37	3	40
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
SRP_00340	Metazoa_SRP links to Rfam database...	0.51	0.56	0.47	46	41230	56	11	41	4	36
SRP_00361	Plant_SRP links to Rfam database...	0.70	0.72	0.68	65	41810	37	6	24	7	25
SRP_00371	Fungi_SRP links to Rfam database...	0.77	0.79	0.76	65	36229	27	2	19	6	17
SRP_00382	Fungi_SRP links to Rfam database...	0.68	0.69	0.66	117	141602	74	10	49	15	53

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

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

Total Base Pair Counts
Total TP	385
Total TN	8672323
Total FP	134
Total FP CONTRA	4
Total FP INCONS	87
Total FP COMP	43
Total FN	13408

Total Scores
MCC	0.150
Average MCC ± 95% Confidence Intervals	0.057 ± 0.030
Sensitivity	0.028
Positive Predictive Value	0.809
Nr of predictions	145

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00001	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	34191	0	0	0	0	75
ASE_00002	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	35511	0	0	0	0	73
ASE_00009	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	26106	0	0	0	0	67
ASE_00014	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	54285	0	0	0	0	106
ASE_00116	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	31626	0	0	0	0	66
ASE_00120	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	46971	0	0	0	0	94
ASE_00121	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	45150	0	0	0	0	92
ASE_00145	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	70125	0	0	0	0	111
ASE_00148	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	112575	0	0	0	0	154
ASE_00154	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	65341	0	0	0	0	107
ASE_00155	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	93528	0	0	0	0	142
ASE_00187	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	68635	0	0	0	0	115
ASE_00191	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	29646	0	0	0	0	61
ASE_00196	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	31626	0	0	0	0	75
ASE_00205	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	90
ASE_00209	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	43071	0	0	0	0	88
ASE_00210	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	27261	0	0	0	0	65
ASE_00213	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	27261	0	0	0	0	66
ASE_00222	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	112101	0	0	0	0	157
ASE_00346	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	48205	0	0	0	0	97
ASE_00359	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	42778	0	0	0	0	80
ASE_00360	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	29403	0	0	0	0	65
ASE_00417	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	54615	0	0	0	0	100
ASE_00418	RNaseP_arch links to Rfam database...	0.00	0.00	0.00	0	38781	0	0	0	0	75
CRW_00013	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	103740	0	0	0	0	115
CRW_00016	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	77421	0	0	0	0	120
CRW_00610	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	36315	0	0	0	0	81
CRW_00613	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	34980	0	0	0	0	78
CRW_00614	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	121771	0	0	0	0	57
CRW_00618	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	56280	0	0	0	0	61
CRW_00619	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	165025	0	0	0	0	73
CRW_00620	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	150975	0	0	0	0	63
CRW_00621	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	153181	0	0	0	0	71
CRW_00623	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	129795	0	0	0	0	83
CRW_00633	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	63546	0	0	0	0	106
CRW_00634	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	64620	0	0	0	0	94
CRW_00670	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	70125	0	0	0	0	120
CRW_00671	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	62835	0	0	0	0	117
CRW_00672	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	72390	0	0	0	0	111
CRW_00674	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	83436	0	0	0	0	124
CRW_00676	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	93528	0	0	0	0	115
CRW_00692	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	68635	0	0	0	0	90
PDB_00827	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	27028	0	0	0	0	81
RFA_00597	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	97903	0	0	0	0	109
RFA_00598	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	84666	0	0	0	0	101
RFA_00599	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	101475	0	0	0	0	111
RFA_00600	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	120295	0	0	0	0	100
RFA_00601	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	99235	0	0	0	0	114
RFA_00602	Telomerase-vert links to Rfam database...	0.00	0.00	0.00	0	101475	0	0	0	0	116
RFA_00606	Telomerase-cil links to Rfam database...	0.17	0.08	0.38	3	21313	6	1	4	1	36
RFA_00620	Telomerase-cil links to Rfam database...	0.13	0.08	0.23	3	21932	11	2	8	1	36
RFA_00621	RNase_MRP links to Rfam database...	0.00	0.00	0.00	0	46360	0	0	0	0	76
RFA_00623	RNase_MRP links to Rfam database...	0.00	0.00	0.00	0	43956	0	0	0	0	78
RFA_00624	RNase_MRP links to Rfam database...	0.00	0.00	0.00	0	30135	0	0	0	0	61
RFA_00626	rne5 links to Rfam database...	0.67	0.52	0.87	45	56564	11	0	7	4	42
RFA_00627	rne5 links to Rfam database...	0.69	0.55	0.86	48	56897	10	0	8	2	39
RFA_00628	rne5 links to Rfam database...	0.66	0.43	1.00	37	57254	6	0	0	6	49
RFA_00630	rne5 links to Rfam database...	0.79	0.67	0.94	58	56891	12	0	4	8	29
RFA_00639	7SK links to Rfam database...	0.00	0.00	0.00	0	54608	7	0	7	0	87
RFA_00805	RNAIII links to Rfam database...	0.09	0.04	0.21	6	133357	23	0	23	0	144
RFA_00814	R2_retro_el links to Rfam database...	0.66	0.44	1.00	18	25182	2	0	0	2	23
RFA_00815	R2_retro_el links to Rfam database...	0.75	0.56	1.00	23	24508	1	0	0	1	18
RFA_00816	R2_retro_el links to Rfam database...	0.66	0.44	1.00	18	23202	2	0	0	2	23
RFA_00817	R2_retro_el links to Rfam database...	0.80	0.66	0.96	27	21917	1	0	1	0	14
RFA_00818	R2_retro_el links to Rfam database...	0.70	0.49	1.00	20	20281	3	0	0	3	21
RFA_00819	R2_retro_el links to Rfam database...	0.75	0.56	1.00	23	27943	2	0	0	2	18
RFA_00820	bicoid_3 links to Rfam database...	0.39	0.19	0.78	31	151485	12	0	9	3	129
RFA_00830	bicoid_3 links to Rfam database...	0.31	0.16	0.60	25	152586	25	1	16	8	129
SRP_00009	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46665	0	0	0	0	102
SRP_00011	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46360	0	0	0	0	104
SRP_00012	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46360	0	0	0	0	101
SRP_00015	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46360	0	0	0	0	99
SRP_00016	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	47895	0	0	0	0	109
SRP_00018	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	38503	0	0	0	0	81
SRP_00019	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	36046	0	0	0	0	91
SRP_00069	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	34453	0	0	0	0	85
SRP_00070	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	126756	0	0	0	0	121
SRP_00073	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	39060	0	0	0	0	71
SRP_00079	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	41905	0	0	0	0	88
SRP_00085	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	45451	0	0	0	0	101
SRP_00087	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	37401	0	0	0	0	58
SRP_00091	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	52975	0	0	0	0	95
SRP_00099	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	44850	0	0	0	0	95
SRP_00104	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	34453	0	0	0	0	69
SRP_00124	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	37128	0	0	0	0	85
SRP_00127	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	72390	0	0	0	0	119
SRP_00130	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	49770	0	0	0	0	97
SRP_00136	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	44253	0	0	0	0	71
SRP_00142	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	93
SRP_00143	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	49770	0	0	0	0	101
SRP_00144	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	46665	0	0	0	0	94
SRP_00148	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	50086	0	0	0	0	87
SRP_00152	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	45753	0	0	0	0	103
SRP_00153	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46971	0	0	0	0	107
SRP_00157	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	44253	0	0	0	0	72
SRP_00158	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	124251	0	0	0	0	115
SRP_00160	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	86320	0	0	0	0	130
SRP_00175	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	44551	0	0	0	0	84
SRP_00178	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	45753	0	0	0	0	102
SRP_00179	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	105
SRP_00181	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	102
SRP_00182	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	101
SRP_00184	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	100
SRP_00188	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	31125	0	0	0	0	79
SRP_00197	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	49455	0	0	0	0	101
SRP_00198	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	51040	0	0	0	0	103
SRP_00199	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	51040	0	0	0	0	105
SRP_00201	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	47895	0	0	0	0	111
SRP_00202	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	54285	0	0	0	0	117
SRP_00203	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	48828	0	0	0	0	105
SRP_00204	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	49141	0	0	0	0	102
SRP_00206	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	47895	0	0	0	0	108
SRP_00230	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	39621	0	0	0	0	90
SRP_00239	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	50403	0	0	0	0	93
SRP_00240	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	48205	0	0	0	0	102
SRP_00241	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	82
SRP_00252	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	49141	0	0	0	0	89
SRP_00253	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	49455	0	0	0	0	90
SRP_00254	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	32385	0	0	0	0	61
SRP_00255	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	47586	0	0	0	0	94
SRP_00257	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	51040	0	0	0	0	108
SRP_00260	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	47895	0	0	0	0	100
SRP_00265	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	41328	0	0	0	0	73
SRP_00276	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	50721	0	0	0	0	110
SRP_00278	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	105
SRP_00286	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	137026	0	0	0	0	174
SRP_00287	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	141778	0	0	0	0	162
SRP_00290	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	100576	0	0	0	0	135
SRP_00292	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	137550	0	0	0	0	173
SRP_00294	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	129286	0	0	0	0	167
SRP_00301	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	32640	0	0	0	0	86
SRP_00302	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	41616	0	0	0	0	81
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	36315	0	0	0	0	88
SRP_00322	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	48516	0	0	0	0	109
SRP_00323	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	47278	0	0	0	0	107
SRP_00328	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	39621	0	0	0	0	85
SRP_00329	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	39903	0	0	0	0	85
SRP_00330	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	50086	0	0	0	0	95
SRP_00331	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	37675	0	0	0	0	87
SRP_00332	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	50403	0	0	0	0	106
SRP_00339	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	44551	0	0	0	0	94
SRP_00340	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	41328	0	0	0	0	82
SRP_00361	Plant_SRP links to Rfam database...	0.00	0.00	0.00	0	41905	0	0	0	0	90
SRP_00371	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	36315	0	0	0	0	82
SRP_00382	Fungi_SRP links to Rfam database...	0.00	0.00	0.00	0	141778	0	0	0	0	170

^top

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 Carnac(seed) - scored lower in this pairwise comparison

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

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