CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	ProbKnot		Carnac(seed)
MCC	0.561	>	0.150
Average MCC ± 95% Confidence Intervals	0.552 ± 0.032	>	0.057 ± 0.030
Sensitivity	0.565	>	0.028
Positive Predictive Value	0.558	<	0.809
Total TP	7795	>	385
Total TN	8658841	<	8672323
Total FP	7641	>	134
Total FP CONTRA	1085	>	4
Total FP INCONS	5078	>	87
Total FP COMP	1478	>	43
Total FN	5998	<	13408
P-value	3.56938820447e-08

^top

Performance plots

Comparison of performance of ProbKnot 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 ProbKnot 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 ProbKnot and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot 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 ProbKnot and Carnac(seed)).

^top

Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	7795
Total TN	8658841
Total FP	7641
Total FP CONTRA	1085
Total FP INCONS	5078
Total FP COMP	1478
Total FN	5998

Total Scores
MCC	0.561
Average MCC ± 95% Confidence Intervals	0.552 ± 0.032
Sensitivity	0.565
Positive Predictive Value	0.558
Nr of predictions	145

^top

2. Individual counts for ProbKnot [ 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...	0.63	0.61	0.65	46	34120	32	4	21	7	29
ASE_00002	RNaseP_arch links to Rfam database...	0.69	0.67	0.71	49	35442	28	4	16	8	24
ASE_00009	RNaseP_arch links to Rfam database...	0.38	0.37	0.40	25	26043	38	5	33	0	42
ASE_00014	RNaseP_arch links to Rfam database...	0.44	0.42	0.46	44	54190	57	2	49	6	62
ASE_00116	RNaseP_arch links to Rfam database...	0.39	0.36	0.43	24	31570	35	4	28	3	42
ASE_00120	RNaseP_arch links to Rfam database...	0.57	0.55	0.60	52	46884	35	7	28	0	42
ASE_00121	RNaseP_arch links to Rfam database...	0.25	0.25	0.26	23	45061	68	5	61	2	69
ASE_00145	RNaseP_arch links to Rfam database...	0.55	0.54	0.57	60	70019	51	7	39	5	51
ASE_00148	RNaseP_arch links to Rfam database...	0.69	0.66	0.73	101	112437	39	4	33	2	53
ASE_00154	RNaseP_arch links to Rfam database...	0.58	0.57	0.59	61	65237	46	4	39	3	46
ASE_00155	RNaseP_arch links to Rfam database...	0.54	0.52	0.56	74	93395	62	10	49	3	68
ASE_00187	RNaseP_arch links to Rfam database...	0.41	0.39	0.43	45	68531	66	7	52	7	70
ASE_00191	RNaseP_arch links to Rfam database...	0.53	0.51	0.56	31	29591	30	2	22	6	30
ASE_00196	RNaseP_arch links to Rfam database...	0.79	0.79	0.79	59	31551	23	2	14	7	16
ASE_00205	RNaseP_arch links to Rfam database...	0.62	0.62	0.62	56	45965	39	6	29	4	34
ASE_00209	RNaseP_arch links to Rfam database...	0.43	0.40	0.46	35	42995	41	6	35	0	53
ASE_00210	RNaseP_arch links to Rfam database...	0.64	0.66	0.62	43	27192	28	6	20	2	22
ASE_00213	RNaseP_arch links to Rfam database...	0.71	0.70	0.73	46	27198	19	3	14	2	20
ASE_00222	RNaseP_arch links to Rfam database...	0.55	0.51	0.59	80	111965	58	5	51	2	77
ASE_00346	RNaseP_arch links to Rfam database...	0.46	0.44	0.48	43	48115	54	4	43	7	54
ASE_00359	RNaseP_arch links to Rfam database...	0.24	0.24	0.24	19	42698	61	7	54	0	61
ASE_00360	RNaseP_arch links to Rfam database...	0.32	0.31	0.33	20	29343	40	8	32	0	45
ASE_00417	RNaseP_arch links to Rfam database...	0.36	0.37	0.35	37	54509	72	11	58	3	63
ASE_00418	RNaseP_arch links to Rfam database...	0.19	0.20	0.19	15	38700	70	8	58	4	60
CRW_00013	Intron_gpI links to Rfam database...	0.39	0.37	0.42	43	103637	84	9	51	24	72
CRW_00016	Intron_gpI links to Rfam database...	0.48	0.45	0.50	54	77314	68	6	47	15	66
CRW_00610	Intron_gpI links to Rfam database...	0.44	0.44	0.43	36	36232	49	8	39	2	45
CRW_00613	Intron_gpI links to Rfam database...	0.84	0.82	0.86	64	34906	18	0	10	8	14
CRW_00614	Intron_gpI links to Rfam database...	0.14	0.16	0.12	9	121698	120	17	47	56	48
CRW_00618	Intron_gpI links to Rfam database...	0.18	0.20	0.16	12	56207	83	15	46	22	49
CRW_00619	Intron_gpI links to Rfam database...	0.35	0.37	0.33	27	164943	151	8	47	96	46
CRW_00620	Intron_gpI links to Rfam database...	0.18	0.21	0.15	13	150891	156	19	52	85	50
CRW_00621	Intron_gpI links to Rfam database...	0.35	0.34	0.36	24	153114	139	8	35	96	47
CRW_00623	Intron_gpI links to Rfam database...	0.31	0.29	0.32	24	129721	122	7	43	72	59
CRW_00633	Intron_gpI links to Rfam database...	0.62	0.59	0.65	63	63449	38	9	25	4	43
CRW_00634	Intron_gpI links to Rfam database...	0.50	0.49	0.52	46	64531	48	10	33	5	48
CRW_00670	Intron_gpI links to Rfam database...	0.57	0.58	0.56	70	70001	57	11	43	3	50
CRW_00671	Intron_gpI links to Rfam database...	0.79	0.77	0.80	90	62723	28	6	16	6	27
CRW_00672	Intron_gpI links to Rfam database...	0.76	0.78	0.74	87	72272	41	10	21	10	24
CRW_00674	Intron_gpI links to Rfam database...	0.68	0.67	0.70	83	83317	41	8	28	5	41
CRW_00676	Intron_gpI links to Rfam database...	0.59	0.58	0.60	67	93416	63	8	37	18	48
CRW_00692	Intron_gpI links to Rfam database...	0.33	0.34	0.32	31	68537	84	18	49	17	59
PDB_00827	Intron_gpI links to Rfam database...	0.76	0.67	0.86	54	26965	11	1	8	2	27
RFA_00597	Telomerase-vert links to Rfam database...	0.24	0.26	0.23	28	97782	111	22	71	18	81
RFA_00598	Telomerase-vert links to Rfam database...	0.62	0.58	0.66	59	84577	56	4	26	26	42
RFA_00599	Telomerase-vert links to Rfam database...	0.73	0.72	0.73	80	101366	58	10	19	29	31
RFA_00600	Telomerase-vert links to Rfam database...	0.62	0.70	0.55	70	120168	100	31	26	43	30
RFA_00601	Telomerase-vert links to Rfam database...	0.49	0.51	0.46	58	99110	84	27	40	17	56
RFA_00602	Telomerase-vert links to Rfam database...	0.66	0.68	0.65	79	101353	63	21	22	20	37
RFA_00606	Telomerase-cil links to Rfam database...	0.60	0.62	0.59	24	21280	33	7	10	16	15
RFA_00620	Telomerase-cil links to Rfam database...	0.43	0.49	0.38	19	21895	44	8	23	13	20
RFA_00621	RNase_MRP links to Rfam database...	0.40	0.41	0.40	31	46282	64	1	46	17	45
RFA_00623	RNase_MRP links to Rfam database...	0.39	0.42	0.35	33	43863	73	4	56	13	45
RFA_00624	RNase_MRP links to Rfam database...	0.43	0.48	0.39	29	30060	53	9	37	7	32
RFA_00626	rne5 links to Rfam database...	0.86	0.80	0.91	70	56539	32	1	6	25	17
RFA_00627	rne5 links to Rfam database...	0.69	0.69	0.68	60	56865	47	6	22	19	27
RFA_00628	rne5 links to Rfam database...	0.90	0.88	0.93	76	57209	31	1	5	25	10
RFA_00630	rne5 links to Rfam database...	0.69	0.66	0.72	57	56874	41	4	18	19	30
RFA_00639	7SK links to Rfam database...	0.57	0.57	0.57	50	54528	49	8	29	12	37
RFA_00805	RNAIII links to Rfam database...	0.73	0.72	0.73	108	133239	49	5	34	10	42
RFA_00814	R2_retro_el links to Rfam database...	0.32	0.37	0.28	15	25146	45	8	31	6	26
RFA_00815	R2_retro_el links to Rfam database...	0.57	0.61	0.54	25	24485	35	5	16	14	16
RFA_00816	R2_retro_el links to Rfam database...	0.80	0.88	0.73	36	23171	20	9	4	7	5
RFA_00817	R2_retro_el links to Rfam database...	0.10	0.12	0.08	5	21883	57	18	39	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.48	0.54	0.43	22	20250	38	13	16	9	19
RFA_00819	R2_retro_el links to Rfam database...	0.96	0.95	0.98	39	27926	34	0	1	33	2
RFA_00820	bicoid_3 links to Rfam database...	0.83	0.83	0.82	133	151363	45	7	22	16	27
RFA_00830	bicoid_3 links to Rfam database...	0.48	0.45	0.51	70	152491	110	5	62	43	84
SRP_00009	Plant_SRP links to Rfam database...	0.47	0.45	0.50	46	46573	46	6	40	0	56
SRP_00011	Plant_SRP links to Rfam database...	0.58	0.56	0.61	58	46265	39	2	35	2	46
SRP_00012	Plant_SRP links to Rfam database...	0.64	0.60	0.69	61	46271	29	1	27	1	40
SRP_00015	Plant_SRP links to Rfam database...	0.83	0.81	0.86	80	46267	23	0	13	10	19
SRP_00016	Archaea_SRP links to Rfam database...	0.79	0.78	0.80	85	47789	22	5	16	1	24
SRP_00018	Fungi_SRP links to Rfam database...	0.56	0.57	0.56	46	38421	46	7	29	10	35
SRP_00019	Fungi_SRP links to Rfam database...	0.90	0.89	0.91	81	35957	15	4	4	7	10
SRP_00069	Fungi_SRP links to Rfam database...	0.72	0.74	0.69	63	34362	31	4	24	3	22
SRP_00070	Fungi_SRP links to Rfam database...	0.28	0.32	0.24	39	126592	133	37	88	8	82
SRP_00073	Fungi_SRP links to Rfam database...	0.64	0.66	0.62	47	38984	42	8	21	13	24
SRP_00079	Plant_SRP links to Rfam database...	0.77	0.80	0.75	70	41812	33	5	18	10	18
SRP_00085	Plant_SRP links to Rfam database...	0.65	0.63	0.67	64	45355	38	7	25	6	37
SRP_00087	Fungi_SRP links to Rfam database...	0.07	0.09	0.06	5	37317	86	24	55	7	53
SRP_00091	Fungi_SRP links to Rfam database...	0.80	0.82	0.78	78	52875	33	4	18	11	17
SRP_00099	Plant_SRP links to Rfam database...	0.60	0.62	0.58	59	44749	44	6	36	2	36
SRP_00104	Fungi_SRP links to Rfam database...	0.40	0.43	0.36	30	34370	60	7	46	7	39
SRP_00124	Metazoa_SRP links to Rfam database...	0.65	0.64	0.68	54	37048	33	1	25	7	31
SRP_00127	Fungi_SRP links to Rfam database...	0.71	0.71	0.70	85	72269	43	7	29	7	34
SRP_00130	Archaea_SRP links to Rfam database...	0.50	0.51	0.49	49	49670	54	9	42	3	48
SRP_00136	Fungi_SRP links to Rfam database...	0.35	0.38	0.33	27	44171	61	13	42	6	44
SRP_00142	Archaea_SRP links to Rfam database...	0.33	0.32	0.34	30	45967	61	8	51	2	63
SRP_00143	Archaea_SRP links to Rfam database...	0.37	0.38	0.36	38	49664	70	7	61	2	63
SRP_00144	Archaea_SRP links to Rfam database...	0.38	0.39	0.38	37	46567	65	9	52	4	57
SRP_00148	Fungi_SRP links to Rfam database...	0.55	0.57	0.53	50	49992	56	3	41	12	37
SRP_00152	Plant_SRP links to Rfam database...	0.69	0.66	0.72	68	45658	33	1	26	6	35
SRP_00153	Plant_SRP links to Rfam database...	0.77	0.77	0.77	82	46864	27	6	19	2	25
SRP_00157	Fungi_SRP links to Rfam database...	0.38	0.42	0.34	30	44165	66	15	43	8	42
SRP_00158	Fungi_SRP links to Rfam database...	0.32	0.38	0.26	44	124083	130	48	76	6	71
SRP_00160	Fungi_SRP links to Rfam database...	0.44	0.44	0.44	57	86190	78	7	66	5	73
SRP_00175	Fungi_SRP links to Rfam database...	0.17	0.18	0.17	15	44462	76	13	61	2	69
SRP_00178	Plant_SRP links to Rfam database...	0.30	0.29	0.30	30	45653	72	4	66	2	72
SRP_00179	Plant_SRP links to Rfam database...	0.72	0.70	0.75	73	45959	28	6	18	4	32
SRP_00181	Plant_SRP links to Rfam database...	0.30	0.29	0.32	30	45961	67	2	63	2	72
SRP_00182	Plant_SRP links to Rfam database...	0.74	0.73	0.76	74	45958	27	3	21	3	27
SRP_00184	Plant_SRP links to Rfam database...	0.31	0.30	0.32	30	45961	68	5	60	3	70
SRP_00188	Plant_SRP links to Rfam database...	0.21	0.20	0.22	16	31051	58	3	55	0	63
SRP_00197	Archaea_SRP links to Rfam database...	0.22	0.21	0.24	21	49368	66	5	61	0	80
SRP_00198	Archaea_SRP links to Rfam database...	0.25	0.24	0.26	25	50945	71	5	65	1	78
SRP_00199	Archaea_SRP links to Rfam database...	0.63	0.63	0.63	66	50936	41	3	35	3	39
SRP_00201	Archaea_SRP links to Rfam database...	0.71	0.70	0.72	78	47786	33	3	28	2	33
SRP_00202	Archaea_SRP links to Rfam database...	0.88	0.87	0.89	102	54170	16	2	11	3	15
SRP_00203	Archaea_SRP links to Rfam database...	0.72	0.74	0.70	78	48717	41	2	31	8	27
SRP_00204	Archaea_SRP links to Rfam database...	0.67	0.67	0.67	68	49040	33	7	26	0	34
SRP_00206	Archaea_SRP links to Rfam database...	0.86	0.88	0.83	95	47781	21	5	14	2	13
SRP_00230	Fungi_SRP links to Rfam database...	0.75	0.76	0.75	68	39530	31	2	21	8	22
SRP_00239	Plant_SRP links to Rfam database...	0.29	0.31	0.28	29	50300	75	16	58	1	64
SRP_00240	Plant_SRP links to Rfam database...	0.65	0.66	0.64	67	48101	45	2	35	8	35
SRP_00241	Plant_SRP links to Rfam database...	0.44	0.48	0.41	39	45960	60	17	40	3	43
SRP_00252	Metazoa_SRP links to Rfam database...	0.50	0.54	0.46	48	49037	59	12	44	3	41
SRP_00253	Metazoa_SRP links to Rfam database...	0.51	0.54	0.47	49	49351	61	9	46	6	41
SRP_00254	Fungi_SRP links to Rfam database...	0.48	0.54	0.43	33	32309	51	12	31	8	28
SRP_00255	Archaea_SRP links to Rfam database...	0.62	0.62	0.62	58	47492	41	3	33	5	36
SRP_00257	Metazoa_SRP links to Rfam database...	0.86	0.86	0.86	93	50932	18	5	10	3	15
SRP_00260	Metazoa_SRP links to Rfam database...	0.62	0.66	0.58	66	47782	50	7	40	3	34
SRP_00265	Fungi_SRP links to Rfam database...	0.58	0.62	0.55	45	41246	50	10	27	13	28
SRP_00276	Archaea_SRP links to Rfam database...	0.85	0.84	0.87	92	50615	17	5	9	3	18
SRP_00278	Archaea_SRP links to Rfam database...	0.67	0.67	0.67	70	45951	38	3	32	3	35
SRP_00286	Fungi_SRP links to Rfam database...	0.62	0.62	0.63	108	136854	73	3	61	9	66
SRP_00287	Fungi_SRP links to Rfam database...	0.59	0.60	0.59	97	141614	77	12	55	10	65
SRP_00290	Fungi_SRP links to Rfam database...	0.67	0.68	0.66	92	100436	63	3	45	15	43
SRP_00292	Fungi_SRP links to Rfam database...	0.55	0.52	0.58	90	137394	73	3	63	7	83
SRP_00294	Fungi_SRP links to Rfam database...	0.59	0.59	0.60	98	129122	70	7	59	4	69
SRP_00301	Fungi_SRP links to Rfam database...	0.85	0.84	0.87	72	32557	19	1	10	8	14
SRP_00302	Fungi_SRP links to Rfam database...	0.38	0.40	0.38	32	41531	62	10	43	9	49
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.73	0.75	0.71	66	36222	30	4	23	3	22
SRP_00322	Archaea_SRP links to Rfam database...	0.66	0.64	0.68	70	48413	34	2	31	1	39
SRP_00323	Archaea_SRP links to Rfam database...	0.82	0.80	0.83	86	47175	20	0	17	3	21
SRP_00328	Metazoa_SRP links to Rfam database...	0.62	0.65	0.59	55	39528	43	10	28	5	30
SRP_00329	Metazoa_SRP links to Rfam database...	0.57	0.58	0.56	49	39816	43	8	30	5	36
SRP_00330	Archaea_SRP links to Rfam database...	0.42	0.39	0.46	37	50006	44	3	40	1	58
SRP_00331	Metazoa_SRP links to Rfam database...	0.54	0.54	0.55	47	37589	42	7	32	3	40
SRP_00332	Archaea_SRP links to Rfam database...	0.69	0.70	0.69	74	50296	35	7	26	2	32
SRP_00339	Archaea_SRP links to Rfam database...	0.70	0.67	0.73	63	44465	27	4	19	4	31
SRP_00340	Metazoa_SRP links to Rfam database...	0.51	0.55	0.47	45	41232	53	10	41	2	37
SRP_00361	Plant_SRP links to Rfam database...	0.75	0.78	0.72	70	41808	37	5	22	10	20
SRP_00371	Fungi_SRP links to Rfam database...	0.78	0.80	0.75	66	36227	32	3	19	10	16
SRP_00382	Fungi_SRP links to Rfam database...	0.56	0.56	0.55	96	141605	88	8	69	11	74

^top

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

^top

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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

2. Individual counts for ProbKnot [ 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 ]