CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PknotsRG		RNAalifold(seed)
MCC	0.527	>	0.469
Average MCC ± 95% Confidence Intervals	0.519 ± 0.019	>	0.462 ± 0.014
Sensitivity	0.516	>	0.272
Positive Predictive Value	0.539	<	0.811
Total TP	14971	>	7873
Total TN	17529149	<	17547235
Total FP	14792	>	2022
Total FP CONTRA	1778	>	261
Total FP INCONS	11040	>	1569
Total FP COMP	1974	>	192
Total FN	14027	<	21125
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of PknotsRG and RNAalifold(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 PknotsRG and RNAalifold(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 PknotsRG and RNAalifold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PknotsRG and RNAalifold(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 PknotsRG and RNAalifold(seed)).

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Performance of PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	14971
Total TN	17529149
Total FP	14792
Total FP CONTRA	1778
Total FP INCONS	11040
Total FP COMP	1974
Total FN	14027

Total Scores
MCC	0.527
Average MCC ± 95% Confidence Intervals	0.519 ± 0.019
Sensitivity	0.516
Positive Predictive Value	0.539
Nr of predictions	278

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2. Individual counts for PknotsRG [ 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	0.64	46	34119	33	3	23	7	29
ASE_00002	RNaseP_arch links to Rfam database...	0.50	0.49	0.51	36	35440	40	5	30	5	37
ASE_00004	RNaseP_bact_a links to Rfam database...	0.70	0.71	0.70	69	47796	32	9	21	2	28
ASE_00005	RNaseP_bact_a links to Rfam database...	0.63	0.58	0.68	68	57870	38	0	32	6	49
ASE_00006	RNaseP_bact_a links to Rfam database...	0.57	0.58	0.57	54	47491	44	7	34	3	39
ASE_00007	RNaseP_bact_a links to Rfam database...	0.57	0.55	0.61	60	59586	43	1	38	4	50
ASE_00009	RNaseP_arch links to Rfam database...	0.78	0.75	0.82	50	26045	13	0	11	2	17
ASE_00012	RNaseP_bact_a links to Rfam database...	0.58	0.54	0.61	67	73811	49	2	40	7	56
ASE_00014	RNaseP_arch links to Rfam database...	0.24	0.25	0.24	26	54178	82	8	73	1	80
ASE_00017	RNaseP_nuc links to Rfam database...	0.14	0.16	0.13	10	50964	85	8	58	19	54
ASE_00018	RNaseP_bact_a links to Rfam database...	0.80	0.76	0.84	102	80479	22	3	17	2	32
ASE_00020	RNaseP_bact_a links to Rfam database...	0.53	0.52	0.53	66	73796	58	8	50	0	60
ASE_00021	RNaseP_bact_a links to Rfam database...	0.57	0.54	0.61	86	104056	61	7	47	7	74
ASE_00022	RNaseP_bact_b links to Rfam database...	0.46	0.44	0.48	54	82915	65	6	53	6	70
ASE_00023	RNaseP_bact_a links to Rfam database...	0.64	0.63	0.65	80	84131	47	5	39	3	47
ASE_00025	RNaseP_nuc links to Rfam database...	0.23	0.24	0.22	17	78528	115	12	49	54	54
ASE_00026	RNaseP_bact_a links to Rfam database...	0.53	0.51	0.54	56	59582	55	1	46	8	54
ASE_00028	RNaseP_bact_b links to Rfam database...	0.59	0.56	0.61	71	84550	53	4	41	8	55
ASE_00029	RNaseP_bact_a links to Rfam database...	0.56	0.54	0.59	66	82916	48	4	42	2	56
ASE_00030	RNaseP_bact_a links to Rfam database...	0.65	0.62	0.68	90	85358	45	3	40	2	55
ASE_00031	RNaseP_bact_a links to Rfam database...	0.63	0.60	0.65	76	86619	50	2	39	9	50
ASE_00032	RNaseP_bact_a links to Rfam database...	0.57	0.54	0.60	64	80094	47	6	36	5	54
ASE_00033	RNaseP_bact_a links to Rfam database...	0.52	0.48	0.57	58	64879	45	5	38	2	63
ASE_00035	RNaseP_bact_a links to Rfam database...	0.30	0.28	0.32	33	70398	76	11	58	7	85
ASE_00036	RNaseP_bact_a links to Rfam database...	0.46	0.45	0.48	59	75731	68	8	57	3	73
ASE_00037	RNaseP_bact_a links to Rfam database...	0.24	0.23	0.25	25	59239	79	3	73	3	85
ASE_00038	RNaseP_bact_a links to Rfam database...	0.55	0.54	0.56	55	53529	45	4	40	1	46
ASE_00040	RNaseP_bact_a links to Rfam database...	0.50	0.47	0.52	63	78882	64	5	53	6	70
ASE_00041	RNaseP_bact_a links to Rfam database...	0.52	0.50	0.55	54	57532	48	2	42	4	54
ASE_00042	RNaseP_bact_a links to Rfam database...	0.53	0.50	0.58	72	89975	54	3	50	1	73
ASE_00044	RNaseP_bact_a links to Rfam database...	0.69	0.68	0.70	71	54513	35	3	28	4	34
ASE_00046	RNaseP_bact_a links to Rfam database...	0.63	0.57	0.69	59	50317	27	2	25	0	44
ASE_00047	RNaseP_bact_a links to Rfam database...	0.33	0.31	0.35	40	74190	76	5	70	1	90
ASE_00052	RNaseP_bact_a links to Rfam database...	0.50	0.46	0.55	52	61330	48	2	41	5	60
ASE_00053	RNaseP_bact_a links to Rfam database...	0.59	0.58	0.60	77	79273	54	5	46	3	56
ASE_00057	RNaseP_bact_a links to Rfam database...	0.63	0.60	0.65	81	82090	49	8	36	5	53
ASE_00064	RNaseP_bact_a links to Rfam database...	0.43	0.43	0.44	38	45364	53	5	44	4	51
ASE_00066	RNaseP_bact_a links to Rfam database...	0.67	0.64	0.71	83	72273	35	4	30	1	47
ASE_00068	RNaseP_bact_a links to Rfam database...	0.24	0.24	0.25	20	37596	59	5	54	0	65
ASE_00069	RNaseP_bact_a links to Rfam database...	0.68	0.65	0.71	91	82899	44	5	33	6	49
ASE_00074	RNaseP_bact_a links to Rfam database...	0.58	0.57	0.59	68	67781	47	6	41	0	51
ASE_00075	RNaseP_bact_a links to Rfam database...	0.65	0.59	0.71	96	108676	46	2	37	7	66
ASE_00076	RNaseP_bact_a links to Rfam database...	0.60	0.57	0.63	67	68158	42	2	38	2	51
ASE_00077	RNaseP_bact_a links to Rfam database...	0.25	0.24	0.25	21	45067	67	7	55	5	65
ASE_00078	RNaseP_bact_a links to Rfam database...	0.68	0.67	0.68	56	42989	31	5	21	5	27
ASE_00079	RNaseP_bact_a links to Rfam database...	0.51	0.50	0.53	50	55517	44	5	39	0	50
ASE_00080	RNaseP_bact_a links to Rfam database...	0.46	0.44	0.48	54	71519	61	5	53	3	69
ASE_00081	RNaseP_bact_a links to Rfam database...	0.53	0.53	0.54	51	49676	44	5	38	1	46
ASE_00082	RNaseP_bact_a links to Rfam database...	0.50	0.47	0.54	54	70400	60	1	45	14	62
ASE_00083	RNaseP_bact_a links to Rfam database...	0.79	0.75	0.83	82	62382	26	2	15	9	28
ASE_00084	RNaseP_bact_a links to Rfam database...	0.70	0.69	0.72	68	53534	29	6	20	3	31
ASE_00087	RNaseP_bact_a links to Rfam database...	0.61	0.58	0.65	83	88283	49	5	39	5	61
ASE_00090	RNaseP_bact_a links to Rfam database...	0.59	0.59	0.59	60	55509	47	2	40	5	41
ASE_00092	RNaseP_bact_a links to Rfam database...	0.73	0.70	0.76	79	63442	30	0	25	5	34
ASE_00096	RNaseP_bact_a links to Rfam database...	0.48	0.47	0.50	54	63437	58	4	51	3	61
ASE_00099	RNaseP_bact_a links to Rfam database...	0.51	0.50	0.53	60	64506	56	6	48	2	60
ASE_00100	RNaseP_nuc links to Rfam database...	0.20	0.22	0.19	17	82125	115	16	57	42	59
ASE_00102	RNaseP_bact_a links to Rfam database...	0.42	0.41	0.44	68	117699	89	8	80	1	98
ASE_00104	RNaseP_bact_a links to Rfam database...	0.65	0.63	0.68	75	64151	36	3	32	1	44
ASE_00105	RNaseP_bact_a links to Rfam database...	0.38	0.36	0.40	40	64160	66	9	52	5	71
ASE_00107	RNaseP_bact_a links to Rfam database...	0.47	0.45	0.50	57	73039	57	2	55	0	70
ASE_00108	RNaseP_nuc links to Rfam database...	0.24	0.29	0.20	18	46881	83	21	51	11	45
ASE_00111	RNaseP_nuc links to Rfam database...	0.14	0.18	0.11	10	49998	88	24	54	10	47
ASE_00112	RNaseP_bact_a links to Rfam database...	0.79	0.75	0.84	87	75362	23	5	12	6	29
ASE_00115	RNaseP_bact_a links to Rfam database...	0.48	0.47	0.49	47	54520	56	1	47	8	54
ASE_00116	RNaseP_arch links to Rfam database...	0.19	0.20	0.19	13	31558	58	2	53	3	53
ASE_00118	RNaseP_bact_a links to Rfam database...	0.45	0.44	0.45	45	60627	57	4	50	3	57
ASE_00119	RNaseP_bact_a links to Rfam database...	0.67	0.65	0.69	70	62734	33	1	30	2	38
ASE_00120	RNaseP_arch links to Rfam database...	0.35	0.34	0.36	32	46883	56	9	47	0	62
ASE_00121	RNaseP_arch links to Rfam database...	0.25	0.25	0.26	23	45061	68	9	57	2	69
ASE_00122	RNaseP_bact_a links to Rfam database...	0.28	0.27	0.28	24	43280	61	4	57	0	64
ASE_00123	RNaseP_bact_a links to Rfam database...	0.40	0.39	0.42	33	38424	50	2	44	4	52
ASE_00125	RNaseP_bact_a links to Rfam database...	0.64	0.63	0.65	55	39255	30	4	26	0	33
ASE_00128	RNaseP_bact_a links to Rfam database...	0.76	0.73	0.80	73	53210	25	2	16	7	27
ASE_00129	RNaseP_bact_a links to Rfam database...	0.52	0.50	0.53	56	62730	53	5	44	4	55
ASE_00131	RNaseP_bact_a links to Rfam database...	0.64	0.58	0.72	49	39272	29	0	19	10	36
ASE_00132	RNaseP_bact_a links to Rfam database...	0.66	0.63	0.68	60	50315	30	4	24	2	35
ASE_00134	RNaseP_bact_a links to Rfam database...	0.56	0.57	0.55	54	50305	49	4	40	5	41
ASE_00135	RNaseP_bact_a links to Rfam database...	0.47	0.46	0.48	50	63085	59	8	47	4	59
ASE_00136	RNaseP_bact_a links to Rfam database...	0.49	0.47	0.51	43	48121	50	1	40	9	49
ASE_00137	RNaseP_bact_a links to Rfam database...	0.44	0.43	0.45	42	48423	53	5	46	2	56
ASE_00138	RNaseP_bact_a links to Rfam database...	0.53	0.52	0.55	42	40393	35	4	31	0	39
ASE_00139	RNaseP_bact_a links to Rfam database...	0.80	0.73	0.88	76	54199	15	2	8	5	28
ASE_00140	RNaseP_bact_a links to Rfam database...	0.69	0.65	0.74	81	70767	33	3	25	5	44
ASE_00142	RNaseP_bact_a links to Rfam database...	0.74	0.70	0.79	85	67054	26	4	18	4	37
ASE_00145	RNaseP_arch links to Rfam database...	0.43	0.42	0.44	47	70019	64	6	53	5	64
ASE_00146	RNaseP_bact_a links to Rfam database...	0.51	0.46	0.56	57	70775	47	0	44	3	67
ASE_00148	RNaseP_arch links to Rfam database...	0.70	0.67	0.73	103	112433	42	4	35	3	51
ASE_00151	RNaseP_bact_a links to Rfam database...	0.42	0.41	0.43	40	51911	52	12	40	0	58
ASE_00153	RNaseP_nuc links to Rfam database...	0.61	0.62	0.61	45	57556	71	2	27	42	28
ASE_00154	RNaseP_arch links to Rfam database...	0.64	0.63	0.65	67	65238	39	4	32	3	40
ASE_00155	RNaseP_arch links to Rfam database...	0.51	0.50	0.52	71	93391	71	10	56	5	71
ASE_00163	RNaseP_bact_a links to Rfam database...	0.29	0.29	0.30	27	53211	72	7	56	9	66
ASE_00165	RNaseP_bact_a links to Rfam database...	0.57	0.55	0.60	56	52881	39	7	31	1	45
ASE_00168	RNaseP_nuc links to Rfam database...	0.23	0.28	0.19	18	60629	92	25	54	13	46
ASE_00169	RNaseP_bact_a links to Rfam database...	0.50	0.49	0.51	52	57190	53	7	42	4	55
ASE_00170	RNaseP_bact_a links to Rfam database...	0.70	0.68	0.72	63	48741	25	2	22	1	30
ASE_00171	RNaseP_bact_a links to Rfam database...	0.71	0.70	0.73	66	48425	25	5	20	0	28
ASE_00172	RNaseP_bact_a links to Rfam database...	0.68	0.66	0.70	70	58896	35	4	26	5	36
ASE_00174	RNaseP_bact_a links to Rfam database...	0.55	0.51	0.59	56	60980	39	3	36	0	53
ASE_00175	RNaseP_bact_a links to Rfam database...	0.44	0.44	0.45	47	59926	62	6	52	4	60
ASE_00176	RNaseP_bact_a links to Rfam database...	0.59	0.55	0.63	61	59934	39	5	31	3	49
ASE_00179	RNaseP_bact_a links to Rfam database...	0.64	0.65	0.62	55	44164	34	7	27	0	29
ASE_00180	RNaseP_bact_a links to Rfam database...	0.72	0.69	0.75	69	51268	29	2	21	6	31
ASE_00181	RNaseP_bact_a links to Rfam database...	0.54	0.53	0.55	56	57528	50	3	43	4	50
ASE_00182	RNaseP_bact_a links to Rfam database...	0.49	0.47	0.51	64	84129	65	6	56	3	72
ASE_00184	RNaseP_bact_a links to Rfam database...	0.63	0.64	0.63	65	54511	39	10	29	0	37
ASE_00185	RNaseP_bact_a links to Rfam database...	0.61	0.59	0.65	75	73420	43	5	36	2	53
ASE_00186	RNaseP_bact_a links to Rfam database...	0.74	0.70	0.78	92	78885	31	3	23	5	40
ASE_00187	RNaseP_arch links to Rfam database...	0.51	0.50	0.52	57	68526	57	7	45	5	58
ASE_00189	RNaseP_bact_b links to Rfam database...	0.57	0.55	0.60	56	63097	42	9	28	5	46
ASE_00190	RNaseP_bact_b links to Rfam database...	0.46	0.44	0.47	40	45366	45	8	37	0	50
ASE_00192	RNaseP_bact_b links to Rfam database...	0.46	0.44	0.48	59	84544	69	10	53	6	74
ASE_00194	RNaseP_bact_b links to Rfam database...	0.46	0.45	0.47	53	73423	64	8	52	4	66
ASE_00196	RNaseP_arch links to Rfam database...	0.70	0.69	0.71	52	31553	24	2	19	3	23
ASE_00197	RNaseP_bact_a links to Rfam database...	0.48	0.46	0.51	66	89124	66	4	59	3	79
ASE_00203	RNaseP_bact_a links to Rfam database...	0.70	0.68	0.72	65	46575	29	6	19	4	31
ASE_00204	RNaseP_bact_b links to Rfam database...	0.63	0.60	0.67	67	67796	38	7	26	5	45
ASE_00205	RNaseP_arch links to Rfam database...	0.56	0.56	0.56	50	45967	44	7	32	5	40
ASE_00209	RNaseP_arch links to Rfam database...	0.28	0.27	0.29	24	42989	58	4	54	0	64
ASE_00210	RNaseP_arch links to Rfam database...	0.59	0.60	0.59	39	27195	28	6	21	1	26
ASE_00212	RNaseP_bact_a links to Rfam database...	0.54	0.52	0.55	77	93822	66	5	57	4	71
ASE_00213	RNaseP_arch links to Rfam database...	0.73	0.73	0.73	48	27195	19	6	12	1	18
ASE_00214	RNaseP_bact_a links to Rfam database...	0.78	0.76	0.80	78	56182	28	3	17	8	25
ASE_00215	RNaseP_bact_a links to Rfam database...	0.55	0.53	0.57	52	48425	42	4	35	3	47
ASE_00216	RNaseP_bact_a links to Rfam database...	0.60	0.61	0.60	50	39256	36	8	26	2	32
ASE_00217	RNaseP_bact_a links to Rfam database...	0.30	0.29	0.32	26	40388	60	6	50	4	64
ASE_00221	RNaseP_bact_a links to Rfam database...	0.40	0.38	0.42	45	64514	65	3	58	4	72
ASE_00222	RNaseP_arch links to Rfam database...	0.62	0.60	0.64	94	111954	55	9	44	2	63
ASE_00227	RNaseP_bact_a links to Rfam database...	0.31	0.29	0.33	39	78884	80	5	75	0	94
ASE_00228	RNaseP_bact_a links to Rfam database...	0.59	0.59	0.58	51	46883	37	14	23	0	35
ASE_00229	RNaseP_bact_a links to Rfam database...	0.58	0.57	0.59	50	42401	39	5	30	4	37
ASE_00231	RNaseP_bact_a links to Rfam database...	0.69	0.69	0.70	66	47801	28	5	23	0	30
ASE_00232	RNaseP_bact_a links to Rfam database...	0.56	0.55	0.57	46	38422	38	3	32	3	38
ASE_00234	RNaseP_bact_a links to Rfam database...	0.52	0.49	0.55	63	75351	56	2	50	4	66
ASE_00237	RNaseP_nuc links to Rfam database...	0.00	0.00	0.00	0	45672	99	25	56	18	56
ASE_00238	RNaseP_bact_a links to Rfam database...	0.48	0.47	0.50	54	64152	58	4	51	3	60
ASE_00240	RNaseP_bact_a links to Rfam database...	0.64	0.62	0.66	58	46577	37	2	28	7	35
ASE_00241	RNaseP_bact_a links to Rfam database...	0.56	0.54	0.58	47	43875	43	0	34	9	40
ASE_00242	RNaseP_bact_a links to Rfam database...	0.72	0.68	0.76	76	60975	27	3	21	3	36
ASE_00246	RNaseP_nuc links to Rfam database...	0.16	0.18	0.15	12	48124	82	19	50	13	55
ASE_00247	RNaseP_nuc links to Rfam database...	0.17	0.19	0.16	12	54210	91	16	47	28	52
ASE_00248	RNaseP_bact_a links to Rfam database...	0.46	0.42	0.49	48	62384	49	3	46	0	66
ASE_00250	RNaseP_bact_a links to Rfam database...	0.61	0.59	0.64	77	78883	46	4	39	3	54
ASE_00252	RNaseP_bact_a links to Rfam database...	0.59	0.56	0.62	94	115289	62	5	52	5	74
ASE_00254	RNaseP_bact_a links to Rfam database...	0.61	0.60	0.63	49	36778	33	5	24	4	33
ASE_00255	RNaseP_bact_a links to Rfam database...	0.47	0.45	0.50	59	74572	60	7	53	0	71
ASE_00257	RNaseP_bact_a links to Rfam database...	0.64	0.64	0.65	62	50944	34	0	34	0	35
ASE_00259	RNaseP_bact_a links to Rfam database...	0.35	0.33	0.36	40	73043	71	8	62	1	81
ASE_00263	RNaseP_bact_a links to Rfam database...	0.62	0.62	0.62	74	70380	47	5	41	1	46
ASE_00264	RNaseP_nuc links to Rfam database...	0.84	0.78	0.90	78	49054	24	0	9	15	22
ASE_00267	RNaseP_bact_a links to Rfam database...	0.46	0.44	0.48	39	45069	51	5	37	9	49
ASE_00270	RNaseP_bact_a links to Rfam database...	0.63	0.62	0.64	79	72267	45	8	36	1	49
ASE_00274	RNaseP_bact_a links to Rfam database...	0.48	0.47	0.50	48	55515	48	8	40	0	55
ASE_00277	RNaseP_bact_a links to Rfam database...	0.39	0.40	0.39	36	48113	58	9	47	2	55
ASE_00279	RNaseP_bact_a links to Rfam database...	0.38	0.36	0.41	36	53213	58	1	51	6	65
ASE_00280	RNaseP_bact_a links to Rfam database...	0.37	0.37	0.38	36	51908	62	6	53	3	62
ASE_00281	RNaseP_bact_a links to Rfam database...	0.54	0.51	0.58	45	44473	39	0	33	6	43
ASE_00282	RNaseP_bact_a links to Rfam database...	0.42	0.41	0.42	52	77692	72	6	65	1	75
ASE_00283	RNaseP_bact_a links to Rfam database...	0.74	0.73	0.76	78	61673	27	5	20	2	29
ASE_00284	RNaseP_bact_a links to Rfam database...	0.62	0.60	0.64	65	58210	43	4	32	7	43
ASE_00285	RNaseP_bact_a links to Rfam database...	0.62	0.58	0.66	71	68899	43	2	34	7	51
ASE_00286	RNaseP_bact_a links to Rfam database...	0.43	0.42	0.43	39	46574	61	3	49	9	53
ASE_00287	RNaseP_bact_a links to Rfam database...	0.59	0.55	0.63	57	54855	40	0	34	6	46
ASE_00288	RNaseP_bact_a links to Rfam database...	0.46	0.45	0.48	42	45968	47	3	43	1	51
ASE_00289	RNaseP_bact_a links to Rfam database...	0.66	0.62	0.71	98	100886	44	4	37	3	59
ASE_00292	RNaseP_bact_a links to Rfam database...	0.71	0.66	0.76	91	81690	34	4	25	5	47
ASE_00294	RNaseP_bact_a links to Rfam database...	0.78	0.74	0.83	127	114328	29	3	23	3	44
ASE_00295	RNaseP_bact_a links to Rfam database...	0.53	0.50	0.57	65	73805	53	5	45	3	66
ASE_00296	RNaseP_bact_a links to Rfam database...	0.31	0.30	0.33	43	91677	88	8	78	2	102
ASE_00297	RNaseP_bact_a links to Rfam database...	0.53	0.53	0.54	52	52878	50	3	42	5	46
ASE_00298	RNaseP_bact_a links to Rfam database...	0.19	0.19	0.19	21	67420	90	9	78	3	92
ASE_00299	RNaseP_bact_a links to Rfam database...	0.55	0.55	0.56	55	49357	48	8	35	5	45
ASE_00313	RNaseP_nuc links to Rfam database...	0.72	0.72	0.73	64	62393	46	6	18	22	25
ASE_00316	RNaseP_nuc links to Rfam database...	0.56	0.57	0.54	56	107777	87	13	34	40	42
ASE_00318	RNaseP_bact_b links to Rfam database...	0.64	0.61	0.67	72	80092	40	13	23	4	46
ASE_00327	RNaseP_nuc links to Rfam database...	0.80	0.78	0.82	69	57207	34	4	11	19	20
ASE_00328	RNaseP_bact_b links to Rfam database...	0.41	0.41	0.41	46	72659	73	3	63	7	66
ASE_00330	RNaseP_nuc links to Rfam database...	0.75	0.74	0.75	67	56191	42	3	19	20	23
ASE_00332	RNaseP_bact_a links to Rfam database...	0.54	0.51	0.57	71	81686	59	2	51	6	67
ASE_00335	RNaseP_bact_b links to Rfam database...	0.52	0.52	0.52	60	75350	64	13	43	8	56
ASE_00337	RNaseP_nuc links to Rfam database...	0.36	0.37	0.36	26	39268	58	4	42	12	45
ASE_00338	RNaseP_nuc links to Rfam database...	0.72	0.69	0.74	68	66338	41	7	17	17	30
ASE_00339	RNaseP_bact_a links to Rfam database...	0.53	0.52	0.53	62	80084	65	5	49	11	57
ASE_00340	RNaseP_bact_a links to Rfam database...	0.71	0.72	0.71	61	45970	34	7	18	9	24
ASE_00342	RNaseP_bact_a links to Rfam database...	0.48	0.45	0.50	52	62378	51	1	50	0	63
ASE_00343	RNaseP_bact_a links to Rfam database...	0.60	0.62	0.58	70	83316	60	9	41	10	43
ASE_00346	RNaseP_arch links to Rfam database...	0.30	0.29	0.31	28	48115	64	7	55	2	69
ASE_00353	RNaseP_bact_a links to Rfam database...	0.46	0.47	0.45	50	57860	60	11	49	0	57
ASE_00359	RNaseP_arch links to Rfam database...	0.49	0.49	0.49	39	42698	46	3	38	5	41
ASE_00360	RNaseP_arch links to Rfam database...	0.30	0.31	0.30	20	29337	50	11	35	4	45
ASE_00361	RNaseP_bact_a links to Rfam database...	0.37	0.36	0.38	46	75345	78	9	66	3	81
ASE_00362	RNaseP_bact_a links to Rfam database...	0.62	0.62	0.63	56	48116	36	6	27	3	35
ASE_00363	RNaseP_bact_a links to Rfam database...	0.54	0.55	0.53	52	51262	46	5	41	0	42
ASE_00364	RNaseP_bact_a links to Rfam database...	0.32	0.31	0.33	33	54184	72	7	61	4	72
ASE_00366	RNaseP_bact_a links to Rfam database...	0.52	0.54	0.50	53	58547	55	12	41	2	45
ASE_00367	RNaseP_bact_a links to Rfam database...	0.33	0.35	0.32	30	42976	65	8	57	0	56
ASE_00369	RNaseP_bact_a links to Rfam database...	0.68	0.67	0.69	72	55841	37	2	30	5	35
ASE_00370	RNaseP_bact_a links to Rfam database...	0.65	0.63	0.66	53	41825	27	5	22	0	31
ASE_00372	RNaseP_bact_a links to Rfam database...	0.72	0.71	0.72	71	51905	30	5	22	3	29
ASE_00374	RNaseP_bact_a links to Rfam database...	0.56	0.56	0.57	49	44764	37	8	29	0	39
ASE_00375	RNaseP_bact_a links to Rfam database...	0.57	0.54	0.60	59	60280	42	6	33	3	51
ASE_00376	RNaseP_bact_a links to Rfam database...	0.52	0.50	0.54	53	56855	48	4	41	3	52
ASE_00377	RNaseP_bact_a links to Rfam database...	0.69	0.66	0.72	71	57531	34	3	25	6	36
ASE_00379	RNaseP_bact_a links to Rfam database...	0.44	0.44	0.45	39	45969	55	7	41	7	50
ASE_00380	RNaseP_bact_a links to Rfam database...	0.46	0.44	0.47	44	54853	54	1	48	5	55
ASE_00382	RNaseP_bact_a links to Rfam database...	0.51	0.51	0.52	43	41822	43	6	34	3	41
ASE_00383	RNaseP_bact_a links to Rfam database...	0.44	0.43	0.45	45	54516	59	4	50	5	60
ASE_00384	RNaseP_bact_a links to Rfam database...	0.73	0.71	0.75	65	48429	27	4	18	5	27
ASE_00385	RNaseP_bact_a links to Rfam database...	0.42	0.43	0.41	35	41819	52	6	45	1	46
ASE_00386	RNaseP_bact_a links to Rfam database...	0.53	0.53	0.53	51	50306	51	4	42	5	45
ASE_00387	RNaseP_bact_a links to Rfam database...	0.36	0.37	0.35	38	55837	70	6	64	0	66
ASE_00388	RNaseP_bact_a links to Rfam database...	0.68	0.67	0.69	60	45666	32	1	26	5	29
ASE_00390	RNaseP_bact_a links to Rfam database...	0.50	0.48	0.53	41	42117	44	6	31	7	44
ASE_00393	RNaseP_bact_a links to Rfam database...	0.36	0.34	0.38	32	47810	59	3	50	6	61
ASE_00394	RNaseP_bact_a links to Rfam database...	0.72	0.72	0.73	67	46879	28	3	22	3	26
ASE_00395	RNaseP_bact_a links to Rfam database...	0.51	0.49	0.53	41	41539	45	1	35	9	43
ASE_00396	RNaseP_bact_a links to Rfam database...	0.37	0.36	0.38	30	41536	55	5	45	5	53
ASE_00397	RNaseP_bact_a links to Rfam database...	0.52	0.51	0.52	54	54511	50	7	43	0	51
ASE_00398	RNaseP_bact_a links to Rfam database...	0.64	0.62	0.66	64	55848	36	1	32	3	40
ASE_00400	RNaseP_bact_a links to Rfam database...	0.53	0.52	0.54	55	57868	48	5	42	1	51
ASE_00401	RNaseP_bact_a links to Rfam database...	0.55	0.56	0.54	70	76898	60	13	47	0	56
ASE_00402	RNaseP_bact_a links to Rfam database...	0.60	0.59	0.61	50	42404	35	4	28	3	35
ASE_00403	RNaseP_bact_a links to Rfam database...	0.47	0.44	0.50	47	55851	51	3	44	4	60
ASE_00404	RNaseP_bact_a links to Rfam database...	0.56	0.55	0.56	47	42987	42	0	37	5	38
ASE_00406	RNaseP_bact_a links to Rfam database...	0.69	0.66	0.72	62	48742	33	2	22	9	32
ASE_00411	RNaseP_bact_a links to Rfam database...	0.26	0.27	0.26	24	49362	69	12	57	0	65
ASE_00412	RNaseP_bact_a links to Rfam database...	0.38	0.37	0.39	39	58212	60	13	47	0	66
ASE_00413	RNaseP_bact_a links to Rfam database...	0.46	0.49	0.43	40	44457	54	14	40	0	41
ASE_00414	RNaseP_bact_a links to Rfam database...	0.37	0.36	0.40	34	46274	59	9	43	7	61
ASE_00415	RNaseP_bact_a links to Rfam database...	0.51	0.51	0.51	53	54843	52	7	43	2	50
ASE_00416	RNaseP_bact_a links to Rfam database...	0.71	0.68	0.75	86	77306	36	1	28	7	41
ASE_00417	RNaseP_arch links to Rfam database...	0.36	0.37	0.35	37	54508	73	10	60	3	63
ASE_00418	RNaseP_arch links to Rfam database...	0.21	0.21	0.21	16	38703	67	8	54	5	59
ASE_00419	RNaseP_bact_a links to Rfam database...	0.76	0.73	0.80	75	54852	23	4	15	4	28
ASE_00422	RNaseP_bact_a links to Rfam database...	0.48	0.47	0.49	44	46881	51	5	41	5	50
ASE_00423	RNaseP_bact_a links to Rfam database...	0.49	0.49	0.50	53	56847	56	9	44	3	56
ASE_00426	RNaseP_bact_a links to Rfam database...	0.40	0.39	0.40	42	60971	62	5	57	0	66
ASE_00428	RNaseP_bact_a links to Rfam database...	0.54	0.52	0.57	65	76521	54	5	45	4	60
ASE_00430	RNaseP_bact_a links to Rfam database...	0.63	0.61	0.66	59	46881	36	5	26	5	38
ASE_00431	RNaseP_bact_a links to Rfam database...	0.64	0.59	0.70	56	46280	36	3	21	12	39
ASE_00434	RNaseP_bact_b links to Rfam database...	0.63	0.60	0.66	66	68165	46	9	25	12	44
ASE_00437	RNaseP_bact_a links to Rfam database...	0.42	0.41	0.44	55	79275	71	4	67	0	80
ASE_00438	RNaseP_bact_a links to Rfam database...	0.43	0.42	0.45	49	65957	60	6	54	0	67
ASE_00441	RNaseP_bact_a links to Rfam database...	0.78	0.74	0.83	83	64161	28	1	16	11	29
ASE_00447	RNaseP_bact_a links to Rfam database...	0.49	0.47	0.52	54	60274	55	1	49	5	62
ASE_00448	RNaseP_bact_a links to Rfam database...	0.22	0.22	0.23	25	64151	91	6	79	6	87
ASE_00451	RNaseP_bact_a links to Rfam database...	0.50	0.47	0.52	59	70763	57	3	51	3	66
CRW_00013	Intron_gpI links to Rfam database...	0.16	0.17	0.15	19	103617	114	25	79	10	96
CRW_00016	Intron_gpI links to Rfam database...	0.64	0.62	0.66	74	77309	50	5	33	12	46
CRW_00610	Intron_gpI links to Rfam database...	0.49	0.49	0.49	40	36233	43	7	35	1	41
CRW_00613	Intron_gpI links to Rfam database...	0.64	0.59	0.69	46	34913	29	1	20	8	32
CRW_00614	Intron_gpI links to Rfam database...	0.09	0.11	0.07	6	121690	145	21	54	70	51
CRW_00618	Intron_gpI links to Rfam database...	0.11	0.11	0.10	7	56211	83	13	49	21	54
CRW_00619	Intron_gpI links to Rfam database...	0.38	0.44	0.34	32	164930	138	28	35	75	41
CRW_00620	Intron_gpI links to Rfam database...	0.16	0.21	0.13	13	150871	158	31	60	67	50
CRW_00621	Intron_gpI links to Rfam database...	0.10	0.10	0.10	7	153109	156	13	52	91	64
CRW_00623	Intron_gpI links to Rfam database...	0.30	0.29	0.32	24	129720	119	11	40	68	59
CRW_00633	Intron_gpI links to Rfam database...	0.50	0.48	0.52	51	63447	50	10	38	2	55
CRW_00634	Intron_gpI links to Rfam database...	0.56	0.60	0.52	56	64513	53	17	34	2	38
CRW_00670	Intron_gpI links to Rfam database...	0.75	0.74	0.77	89	70009	30	5	22	3	31
CRW_00671	Intron_gpI links to Rfam database...	0.77	0.76	0.78	89	62721	30	6	19	5	28
CRW_00672	Intron_gpI links to Rfam database...	0.53	0.55	0.52	61	72273	60	21	35	4	50
CRW_00674	Intron_gpI links to Rfam database...	0.52	0.52	0.52	65	83310	63	12	49	2	59
CRW_00676	Intron_gpI links to Rfam database...	0.56	0.60	0.52	69	93396	67	13	50	4	46
CRW_00692	Intron_gpI links to Rfam database...	0.43	0.46	0.41	41	68536	66	18	40	8	49
PDB_00827	Intron_gpI links to Rfam database...	0.50	0.46	0.55	37	26961	31	1	29	1	44
PDB_00919	RNaseP_bact_a links to Rfam database...	0.50	0.47	0.54	48	44164	44	3	38	3	55
RFA_00597	Telomerase-vert links to Rfam database...	0.52	0.53	0.51	58	97789	83	8	48	27	51
RFA_00598	Telomerase-vert links to Rfam database...	0.68	0.66	0.69	67	84569	57	6	24	27	34
RFA_00599	Telomerase-vert links to Rfam database...	0.63	0.68	0.60	75	101349	70	18	33	19	36
RFA_00600	Telomerase-vert links to Rfam database...	0.63	0.70	0.56	70	120170	88	32	23	33	30
RFA_00601	Telomerase-vert links to Rfam database...	0.48	0.50	0.46	57	99111	86	21	46	19	57
RFA_00602	Telomerase-vert links to Rfam database...	0.69	0.72	0.67	83	101351	61	10	31	20	33
TMR_00173	tmRNA links to Rfam database...	0.31	0.36	0.28	15	42141	67	16	23	28	27
TMR_00357	tmRNA links to Rfam database...	0.40	0.41	0.39	38	82931	75	22	37	16	54
TMR_00601	tmRNA links to Rfam database...	0.56	0.57	0.55	24	58952	77	2	18	57	18
TMR_00696	tmRNA links to Rfam database...	0.12	0.12	0.11	14	84955	125	19	90	16	100

^top

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

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

Total Base Pair Counts
Total TP	7873
Total TN	17547235
Total FP	2022
Total FP CONTRA	261
Total FP INCONS	1569
Total FP COMP	192
Total FN	21125

Total Scores
MCC	0.469
Average MCC ± 95% Confidence Intervals	0.462 ± 0.014
Sensitivity	0.272
Positive Predictive Value	0.811
Nr of predictions	278

^top

2. Individual counts for RNAalifold(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...	0.77	0.59	1.00	44	34147	0	0	0	0	31
ASE_00002	RNaseP_arch links to Rfam database...	0.78	0.60	1.00	44	35467	0	0	0	0	29
ASE_00004	RNaseP_bact_a links to Rfam database...	0.45	0.23	0.88	22	47870	3	0	3	0	75
ASE_00005	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.79	30	57932	8	1	7	0	87
ASE_00006	RNaseP_bact_a links to Rfam database...	0.42	0.22	0.83	20	47562	4	0	4	0	73
ASE_00007	RNaseP_bact_a links to Rfam database...	0.52	0.33	0.82	36	59641	8	1	7	0	74
ASE_00009	RNaseP_arch links to Rfam database...	0.74	0.60	0.93	40	26063	3	0	3	0	27
ASE_00012	RNaseP_bact_a links to Rfam database...	0.46	0.26	0.80	32	73880	11	1	7	3	91
ASE_00014	RNaseP_arch links to Rfam database...	0.70	0.52	0.95	55	54227	3	0	3	0	51
ASE_00017	RNaseP_nuc links to Rfam database...	0.51	0.31	0.83	20	51016	5	0	4	1	44
ASE_00018	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.82	36	80557	8	1	7	0	98
ASE_00020	RNaseP_bact_a links to Rfam database...	0.36	0.17	0.73	22	73890	8	3	5	0	104
ASE_00021	RNaseP_bact_a links to Rfam database...	0.39	0.18	0.83	29	104161	6	1	5	0	131
ASE_00022	RNaseP_bact_b links to Rfam database...	0.65	0.48	0.89	59	82962	13	1	6	6	65
ASE_00023	RNaseP_bact_a links to Rfam database...	0.39	0.21	0.71	27	84217	13	1	10	2	100
ASE_00025	RNaseP_nuc links to Rfam database...	0.48	0.28	0.83	20	78582	5	0	4	1	51
ASE_00026	RNaseP_bact_a links to Rfam database...	0.49	0.31	0.77	34	59641	10	1	9	0	76
ASE_00028	RNaseP_bact_b links to Rfam database...	0.65	0.48	0.90	60	84599	12	1	6	5	66
ASE_00029	RNaseP_bact_a links to Rfam database...	0.30	0.14	0.65	17	83002	10	1	8	1	105
ASE_00030	RNaseP_bact_a links to Rfam database...	0.46	0.25	0.86	36	85449	6	1	5	0	109
ASE_00031	RNaseP_bact_a links to Rfam database...	0.37	0.20	0.68	25	86699	12	1	11	0	101
ASE_00032	RNaseP_bact_a links to Rfam database...	0.22	0.09	0.50	11	80178	12	1	10	1	107
ASE_00033	RNaseP_bact_a links to Rfam database...	0.48	0.29	0.81	35	64937	8	1	7	0	86
ASE_00035	RNaseP_bact_a links to Rfam database...	0.47	0.28	0.80	33	70459	11	1	7	3	85
ASE_00036	RNaseP_bact_a links to Rfam database...	0.41	0.22	0.78	29	75818	8	1	7	0	103
ASE_00037	RNaseP_bact_a links to Rfam database...	0.51	0.32	0.81	35	59297	8	1	7	0	75
ASE_00038	RNaseP_bact_a links to Rfam database...	0.42	0.23	0.79	23	53599	6	1	5	0	78
ASE_00040	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.82	36	78959	8	1	7	0	97
ASE_00041	RNaseP_bact_a links to Rfam database...	0.49	0.28	0.88	30	57596	4	0	4	0	78
ASE_00042	RNaseP_bact_a links to Rfam database...	0.41	0.23	0.75	33	90056	11	1	10	0	112
ASE_00044	RNaseP_bact_a links to Rfam database...	0.52	0.33	0.81	35	54572	8	1	7	0	70
ASE_00046	RNaseP_bact_a links to Rfam database...	0.53	0.34	0.81	35	50360	8	1	7	0	68
ASE_00047	RNaseP_bact_a links to Rfam database...	0.36	0.20	0.67	26	74266	13	1	12	0	104
ASE_00052	RNaseP_bact_a links to Rfam database...	0.49	0.30	0.79	34	61382	9	1	8	0	78
ASE_00053	RNaseP_bact_a links to Rfam database...	0.42	0.23	0.79	30	79363	8	1	7	0	103
ASE_00057	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.82	36	82171	8	1	7	0	98
ASE_00064	RNaseP_bact_a links to Rfam database...	0.44	0.25	0.79	22	45423	6	1	5	0	67
ASE_00066	RNaseP_bact_a links to Rfam database...	0.43	0.24	0.79	31	72351	8	1	7	0	99
ASE_00068	RNaseP_bact_a links to Rfam database...	0.37	0.20	0.68	17	37650	8	1	7	0	68
ASE_00069	RNaseP_bact_a links to Rfam database...	0.45	0.25	0.81	35	82985	9	1	7	1	105
ASE_00074	RNaseP_bact_a links to Rfam database...	0.50	0.30	0.82	36	67852	8	1	7	0	83
ASE_00075	RNaseP_bact_a links to Rfam database...	0.38	0.19	0.79	30	108773	13	1	7	5	132
ASE_00076	RNaseP_bact_a links to Rfam database...	0.39	0.19	0.79	23	68236	6	1	5	0	95
ASE_00077	RNaseP_bact_a links to Rfam database...	0.40	0.21	0.75	18	45126	6	1	5	0	68
ASE_00078	RNaseP_bact_a links to Rfam database...	0.49	0.28	0.85	23	43044	6	0	4	2	60
ASE_00079	RNaseP_bact_a links to Rfam database...	0.43	0.23	0.79	23	55582	6	1	5	0	77
ASE_00080	RNaseP_bact_a links to Rfam database...	0.23	0.11	0.48	14	71602	15	1	14	0	109
ASE_00081	RNaseP_bact_a links to Rfam database...	0.43	0.24	0.79	23	49741	6	1	5	0	74
ASE_00082	RNaseP_bact_a links to Rfam database...	0.34	0.16	0.75	18	70476	6	1	5	0	98
ASE_00083	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.79	23	62452	6	1	5	0	87
ASE_00084	RNaseP_bact_a links to Rfam database...	0.43	0.23	0.79	23	53599	6	1	5	0	76
ASE_00087	RNaseP_bact_a links to Rfam database...	0.36	0.16	0.79	23	88381	6	1	5	0	121
ASE_00090	RNaseP_bact_a links to Rfam database...	0.42	0.23	0.79	23	55582	6	1	5	0	78
ASE_00092	RNaseP_bact_a links to Rfam database...	0.40	0.20	0.79	23	63517	6	1	5	0	90
ASE_00096	RNaseP_bact_a links to Rfam database...	0.40	0.20	0.79	23	63517	6	1	5	0	92
ASE_00099	RNaseP_bact_a links to Rfam database...	0.49	0.30	0.82	36	64576	8	1	7	0	84
ASE_00100	RNaseP_nuc links to Rfam database...	0.47	0.26	0.83	20	82191	5	0	4	1	56
ASE_00102	RNaseP_bact_a links to Rfam database...	0.36	0.18	0.71	30	117813	12	1	11	0	136
ASE_00104	RNaseP_bact_a links to Rfam database...	0.50	0.30	0.82	36	64217	8	1	7	0	83
ASE_00105	RNaseP_bact_a links to Rfam database...	0.38	0.20	0.73	22	64231	8	3	5	0	89
ASE_00107	RNaseP_bact_a links to Rfam database...	0.48	0.28	0.82	36	73109	8	1	7	0	91
ASE_00108	RNaseP_nuc links to Rfam database...	0.51	0.32	0.83	20	46947	5	0	4	1	43
ASE_00111	RNaseP_nuc links to Rfam database...	0.52	0.32	0.86	18	50065	3	0	3	0	39
ASE_00112	RNaseP_bact_a links to Rfam database...	0.33	0.19	0.58	22	75428	16	1	15	0	94
ASE_00115	RNaseP_bact_a links to Rfam database...	0.41	0.22	0.79	22	54587	6	1	5	0	79
ASE_00116	RNaseP_arch links to Rfam database...	0.82	0.68	0.98	45	31580	1	0	1	0	21
ASE_00118	RNaseP_bact_a links to Rfam database...	0.41	0.22	0.79	22	60698	7	1	5	1	80
ASE_00119	RNaseP_bact_a links to Rfam database...	0.31	0.12	0.81	13	62819	3	1	2	0	95
ASE_00120	RNaseP_arch links to Rfam database...	0.76	0.59	0.98	55	46915	2	0	1	1	39
ASE_00121	RNaseP_arch links to Rfam database...	0.77	0.61	0.98	56	45093	1	0	1	0	36
ASE_00122	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.79	23	43336	6	1	5	0	65
ASE_00123	RNaseP_bact_a links to Rfam database...	0.38	0.20	0.74	17	38480	6	1	5	0	68
ASE_00125	RNaseP_bact_a links to Rfam database...	0.37	0.16	0.88	14	39324	2	0	2	0	74
ASE_00128	RNaseP_bact_a links to Rfam database...	0.44	0.22	0.88	22	53276	3	1	2	0	78
ASE_00129	RNaseP_bact_a links to Rfam database...	0.40	0.21	0.79	23	62806	6	1	5	0	88
ASE_00131	RNaseP_bact_a links to Rfam database...	0.38	0.20	0.71	17	39316	7	2	5	0	68
ASE_00132	RNaseP_bact_a links to Rfam database...	0.43	0.24	0.77	23	50373	7	2	5	0	72
ASE_00134	RNaseP_bact_a links to Rfam database...	0.44	0.24	0.79	23	50374	6	1	5	0	72
ASE_00135	RNaseP_bact_a links to Rfam database...	0.37	0.19	0.72	21	63161	8	1	7	0	88
ASE_00136	RNaseP_bact_a links to Rfam database...	0.44	0.25	0.79	23	48176	6	1	5	0	69
ASE_00137	RNaseP_bact_a links to Rfam database...	0.44	0.22	0.85	22	48490	4	0	4	0	76
ASE_00138	RNaseP_bact_a links to Rfam database...	0.47	0.28	0.79	23	40441	6	1	5	0	58
ASE_00139	RNaseP_bact_a links to Rfam database...	0.42	0.22	0.79	23	54256	6	1	5	0	81
ASE_00140	RNaseP_bact_a links to Rfam database...	0.36	0.18	0.73	22	70846	8	3	5	0	103
ASE_00142	RNaseP_bact_a links to Rfam database...	0.50	0.30	0.84	36	67118	7	1	6	0	86
ASE_00145	RNaseP_arch links to Rfam database...	0.73	0.54	1.00	60	70065	0	0	0	0	51
ASE_00146	RNaseP_bact_a links to Rfam database...	0.49	0.29	0.82	36	70832	8	1	7	0	88
ASE_00148	RNaseP_arch links to Rfam database...	0.59	0.37	0.95	57	112515	3	0	3	0	97
ASE_00151	RNaseP_bact_a links to Rfam database...	0.55	0.37	0.82	36	51959	8	1	7	0	62
ASE_00153	RNaseP_nuc links to Rfam database...	0.37	0.21	0.68	15	57608	7	0	7	0	58
ASE_00154	RNaseP_arch links to Rfam database...	0.71	0.53	0.95	57	65281	3	0	3	0	50
ASE_00155	RNaseP_arch links to Rfam database...	0.65	0.42	1.00	60	93468	0	0	0	0	82
ASE_00163	RNaseP_bact_a links to Rfam database...	0.44	0.25	0.79	23	53272	6	1	5	0	70
ASE_00165	RNaseP_bact_a links to Rfam database...	0.40	0.20	0.80	20	52950	5	1	4	0	81
ASE_00168	RNaseP_nuc links to Rfam database...	0.51	0.31	0.83	20	60702	5	0	4	1	44
ASE_00169	RNaseP_bact_a links to Rfam database...	0.35	0.19	0.67	20	57261	10	2	8	0	87
ASE_00170	RNaseP_bact_a links to Rfam database...	0.44	0.25	0.79	23	48799	6	1	5	0	70
ASE_00171	RNaseP_bact_a links to Rfam database...	0.44	0.24	0.79	23	48487	6	1	5	0	71
ASE_00172	RNaseP_bact_a links to Rfam database...	0.41	0.22	0.79	23	58967	6	1	5	0	83
ASE_00174	RNaseP_bact_a links to Rfam database...	0.39	0.20	0.76	22	61046	7	2	5	0	87
ASE_00175	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.77	23	60001	7	2	5	0	84
ASE_00176	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.79	23	60002	6	1	5	0	87
ASE_00179	RNaseP_bact_a links to Rfam database...	0.39	0.20	0.77	17	44231	5	1	4	0	67
ASE_00180	RNaseP_bact_a links to Rfam database...	0.42	0.23	0.77	23	51330	7	2	5	0	77
ASE_00181	RNaseP_bact_a links to Rfam database...	0.41	0.22	0.77	23	57600	7	2	5	0	83
ASE_00182	RNaseP_bact_a links to Rfam database...	0.37	0.17	0.79	23	84226	6	1	5	0	113
ASE_00184	RNaseP_bact_a links to Rfam database...	0.42	0.23	0.79	23	54586	6	1	5	0	79
ASE_00185	RNaseP_bact_a links to Rfam database...	0.38	0.18	0.79	23	73507	6	1	5	0	105
ASE_00186	RNaseP_bact_a links to Rfam database...	0.43	0.25	0.75	33	78959	11	1	10	0	99
ASE_00187	RNaseP_arch links to Rfam database...	0.65	0.46	0.91	53	68577	5	1	4	0	62
ASE_00189	RNaseP_bact_b links to Rfam database...	0.66	0.52	0.84	53	63127	15	1	9	5	49
ASE_00190	RNaseP_bact_b links to Rfam database...	0.66	0.50	0.87	45	45399	12	1	6	5	45
ASE_00192	RNaseP_bact_b links to Rfam database...	0.48	0.32	0.70	43	84605	22	1	17	4	90
ASE_00194	RNaseP_bact_b links to Rfam database...	0.63	0.45	0.87	54	73474	13	1	7	5	65
ASE_00196	RNaseP_arch links to Rfam database...	0.77	0.63	0.96	47	31577	2	0	2	0	28
ASE_00197	RNaseP_bact_a links to Rfam database...	0.41	0.23	0.75	33	89209	11	1	10	0	112
ASE_00203	RNaseP_bact_a links to Rfam database...	0.40	0.21	0.77	20	46639	6	2	4	0	76
ASE_00204	RNaseP_bact_b links to Rfam database...	0.67	0.50	0.89	56	67833	13	1	6	6	56
ASE_00205	RNaseP_arch links to Rfam database...	0.77	0.60	1.00	54	46002	1	0	0	1	36
ASE_00209	RNaseP_arch links to Rfam database...	0.79	0.64	0.98	56	43014	1	0	1	0	32
ASE_00210	RNaseP_arch links to Rfam database...	0.68	0.55	0.84	36	27218	9	0	7	2	29
ASE_00212	RNaseP_bact_a links to Rfam database...	0.40	0.22	0.74	32	93918	11	1	10	0	116
ASE_00213	RNaseP_arch links to Rfam database...	0.78	0.62	0.98	41	27219	3	0	1	2	25
ASE_00214	RNaseP_bact_a links to Rfam database...	0.35	0.17	0.72	18	56255	7	2	5	0	85
ASE_00215	RNaseP_bact_a links to Rfam database...	0.36	0.17	0.74	17	48493	6	1	5	0	82
ASE_00216	RNaseP_bact_a links to Rfam database...	0.46	0.24	0.87	20	39317	3	0	3	0	62
ASE_00217	RNaseP_bact_a links to Rfam database...	0.51	0.33	0.79	30	40432	8	1	7	0	60
ASE_00221	RNaseP_bact_a links to Rfam database...	0.50	0.31	0.82	36	64576	8	1	7	0	81
ASE_00222	RNaseP_arch links to Rfam database...	0.62	0.38	1.00	60	112041	0	0	0	0	97
ASE_00227	RNaseP_bact_a links to Rfam database...	0.37	0.20	0.68	27	78963	13	1	12	0	106
ASE_00228	RNaseP_bact_a links to Rfam database...	0.47	0.26	0.88	22	46946	3	0	3	0	64
ASE_00229	RNaseP_bact_a links to Rfam database...	0.47	0.25	0.88	22	42461	3	0	3	0	65
ASE_00231	RNaseP_bact_a links to Rfam database...	0.45	0.23	0.88	22	47870	3	0	3	0	74
ASE_00232	RNaseP_bact_a links to Rfam database...	0.48	0.26	0.88	22	38478	3	0	3	0	62
ASE_00234	RNaseP_bact_a links to Rfam database...	0.35	0.17	0.73	22	75436	8	3	5	0	107
ASE_00237	RNaseP_nuc links to Rfam database...	0.52	0.32	0.86	18	45732	3	0	3	0	38
ASE_00238	RNaseP_bact_a links to Rfam database...	0.38	0.19	0.73	22	64231	8	3	5	0	92
ASE_00240	RNaseP_bact_a links to Rfam database...	0.33	0.18	0.59	17	46636	12	1	11	0	76
ASE_00241	RNaseP_bact_a links to Rfam database...	0.46	0.26	0.79	23	43927	6	1	5	0	64
ASE_00242	RNaseP_bact_a links to Rfam database...	0.51	0.32	0.82	36	61031	8	1	7	0	76
ASE_00246	RNaseP_nuc links to Rfam database...	0.57	0.33	1.00	22	48183	0	0	0	0	45
ASE_00247	RNaseP_nuc links to Rfam database...	0.51	0.31	0.83	20	54261	5	0	4	1	44
ASE_00248	RNaseP_bact_a links to Rfam database...	0.51	0.32	0.82	36	62437	8	1	7	0	78
ASE_00250	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.81	35	78960	8	1	7	0	96
ASE_00252	RNaseP_bact_a links to Rfam database...	0.38	0.18	0.79	31	115401	12	1	7	4	137
ASE_00254	RNaseP_bact_a links to Rfam database...	0.49	0.27	0.88	22	36831	3	0	3	0	60
ASE_00255	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.81	35	74648	8	1	7	0	95
ASE_00257	RNaseP_bact_a links to Rfam database...	0.43	0.24	0.79	23	51011	6	1	5	0	74
ASE_00259	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.80	33	73112	8	1	7	0	88
ASE_00263	RNaseP_bact_a links to Rfam database...	0.39	0.19	0.79	23	70471	6	1	5	0	97
ASE_00264	RNaseP_nuc links to Rfam database...	0.50	0.25	1.00	25	49116	0	0	0	0	75
ASE_00267	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.79	23	45121	6	1	5	0	65
ASE_00270	RNaseP_bact_a links to Rfam database...	0.22	0.09	0.52	12	72367	12	1	10	1	116
ASE_00274	RNaseP_bact_a links to Rfam database...	0.40	0.21	0.73	22	55581	8	3	5	0	81
ASE_00277	RNaseP_bact_a links to Rfam database...	0.42	0.24	0.73	22	48175	8	3	5	0	69
ASE_00279	RNaseP_bact_a links to Rfam database...	0.42	0.23	0.79	23	53272	6	1	5	0	78
ASE_00280	RNaseP_bact_a links to Rfam database...	0.40	0.18	0.86	18	51982	3	1	2	0	80
ASE_00281	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.79	23	44522	6	1	5	0	65
ASE_00282	RNaseP_bact_a links to Rfam database...	0.37	0.18	0.77	23	77785	7	2	5	0	104
ASE_00283	RNaseP_bact_a links to Rfam database...	0.35	0.17	0.75	18	61752	6	1	5	0	89
ASE_00284	RNaseP_bact_a links to Rfam database...	0.40	0.21	0.77	23	58281	7	2	5	0	85
ASE_00285	RNaseP_bact_a links to Rfam database...	0.39	0.19	0.79	23	68977	6	1	5	0	99
ASE_00286	RNaseP_bact_a links to Rfam database...	0.43	0.24	0.79	22	46637	6	1	5	0	70
ASE_00287	RNaseP_bact_a links to Rfam database...	0.42	0.22	0.79	23	54917	6	1	5	0	80
ASE_00288	RNaseP_bact_a links to Rfam database...	0.43	0.25	0.77	23	46026	7	2	5	0	70
ASE_00289	RNaseP_bact_a links to Rfam database...	0.43	0.22	0.81	35	100982	8	1	7	0	122
ASE_00292	RNaseP_bact_a links to Rfam database...	0.46	0.26	0.82	36	81766	8	1	7	0	102
ASE_00294	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.82	36	114437	8	1	7	0	135
ASE_00295	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.82	36	73876	8	1	7	0	95
ASE_00296	RNaseP_bact_a links to Rfam database...	0.45	0.25	0.82	36	91762	8	1	7	0	109
ASE_00297	RNaseP_bact_a links to Rfam database...	0.43	0.23	0.79	23	52946	6	1	5	0	75
ASE_00298	RNaseP_bact_a links to Rfam database...	0.40	0.20	0.79	23	67499	6	1	5	0	90
ASE_00299	RNaseP_bact_a links to Rfam database...	0.39	0.23	0.66	23	49420	12	1	11	0	77
ASE_00313	RNaseP_nuc links to Rfam database...	0.32	0.15	0.68	13	62462	8	2	4	2	76
ASE_00316	RNaseP_nuc links to Rfam database...	0.22	0.07	0.70	7	107870	4	0	3	1	91
ASE_00318	RNaseP_bact_b links to Rfam database...	0.66	0.48	0.89	57	80136	13	1	6	6	61
ASE_00327	RNaseP_nuc links to Rfam database...	0.45	0.21	0.95	19	57271	6	0	1	5	70
ASE_00328	RNaseP_bact_b links to Rfam database...	0.69	0.54	0.90	60	72704	12	1	6	5	52
ASE_00330	RNaseP_nuc links to Rfam database...	0.53	0.28	1.00	25	56255	0	0	0	0	65
ASE_00332	RNaseP_bact_a links to Rfam database...	0.46	0.26	0.82	36	81766	8	1	7	0	102
ASE_00335	RNaseP_bact_b links to Rfam database...	0.68	0.52	0.90	60	75399	12	1	6	5	56
ASE_00337	RNaseP_nuc links to Rfam database...	0.48	0.25	0.90	18	39320	7	0	2	5	53
ASE_00338	RNaseP_nuc links to Rfam database...	0.33	0.14	0.78	14	66412	4	0	4	0	84
ASE_00339	RNaseP_bact_a links to Rfam database...	0.48	0.29	0.81	34	80158	9	1	7	1	85
ASE_00340	RNaseP_bact_a links to Rfam database...	0.43	0.21	0.86	18	46035	3	0	3	0	67
ASE_00342	RNaseP_bact_a links to Rfam database...	0.51	0.31	0.82	36	62437	8	1	7	0	79
ASE_00343	RNaseP_bact_a links to Rfam database...	0.31	0.16	0.60	18	83406	12	2	10	0	95
ASE_00346	RNaseP_arch links to Rfam database...	0.57	0.44	0.74	43	48147	15	0	15	0	54
ASE_00353	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.77	23	57940	7	2	5	0	84
ASE_00359	RNaseP_arch links to Rfam database...	0.73	0.55	0.98	44	42733	2	0	1	1	36
ASE_00360	RNaseP_arch links to Rfam database...	0.82	0.69	0.98	45	29357	1	0	1	0	20
ASE_00361	RNaseP_bact_a links to Rfam database...	0.36	0.17	0.76	22	75437	7	2	5	0	105
ASE_00362	RNaseP_bact_a links to Rfam database...	0.45	0.25	0.79	23	48176	6	1	5	0	68
ASE_00363	RNaseP_bact_a links to Rfam database...	0.44	0.24	0.79	23	51331	6	1	5	0	71
ASE_00364	RNaseP_bact_a links to Rfam database...	0.41	0.22	0.77	23	54255	7	2	5	0	82
ASE_00366	RNaseP_bact_a links to Rfam database...	0.36	0.18	0.72	18	58628	7	2	5	0	80
ASE_00367	RNaseP_bact_a links to Rfam database...	0.46	0.27	0.79	23	43042	6	1	5	0	63
ASE_00369	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.79	23	55916	6	1	5	0	84
ASE_00370	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.76	22	41876	7	1	6	0	62
ASE_00372	RNaseP_bact_a links to Rfam database...	0.41	0.22	0.76	22	51974	7	1	6	0	78
ASE_00374	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.79	23	44821	6	1	5	0	65
ASE_00375	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.79	23	60349	6	1	5	0	87
ASE_00376	RNaseP_bact_a links to Rfam database...	0.42	0.22	0.79	23	56924	6	1	5	0	82
ASE_00377	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.77	23	57600	7	2	5	0	84
ASE_00379	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.79	23	46027	6	1	5	0	66
ASE_00380	RNaseP_bact_a links to Rfam database...	0.43	0.23	0.79	23	54917	6	1	5	0	76
ASE_00382	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.79	23	41876	6	1	5	0	61
ASE_00383	RNaseP_bact_a links to Rfam database...	0.42	0.22	0.79	23	54586	6	1	5	0	82
ASE_00384	RNaseP_bact_a links to Rfam database...	0.44	0.25	0.79	23	48487	6	1	5	0	69
ASE_00385	RNaseP_bact_a links to Rfam database...	0.43	0.26	0.72	21	41876	8	1	7	0	60
ASE_00386	RNaseP_bact_a links to Rfam database...	0.44	0.24	0.79	23	50374	6	1	5	0	73
ASE_00387	RNaseP_bact_a links to Rfam database...	0.38	0.20	0.72	21	55916	8	1	7	0	83
ASE_00388	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.79	23	45724	6	1	5	0	66
ASE_00390	RNaseP_bact_a links to Rfam database...	0.46	0.27	0.79	23	42166	6	1	5	0	62
ASE_00393	RNaseP_bact_a links to Rfam database...	0.40	0.23	0.72	21	47866	8	1	7	0	72
ASE_00394	RNaseP_bact_a links to Rfam database...	0.44	0.25	0.79	23	46942	6	1	5	0	70
ASE_00395	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.79	23	41587	6	1	5	0	61
ASE_00396	RNaseP_bact_a links to Rfam database...	0.47	0.28	0.79	23	41587	6	1	5	0	60
ASE_00397	RNaseP_bact_a links to Rfam database...	0.42	0.22	0.79	23	54586	6	1	5	0	82
ASE_00398	RNaseP_bact_a links to Rfam database...	0.42	0.22	0.79	23	55916	6	1	5	0	81
ASE_00400	RNaseP_bact_a links to Rfam database...	0.41	0.22	0.79	23	57941	6	1	5	0	83
ASE_00401	RNaseP_bact_a links to Rfam database...	0.33	0.14	0.75	18	77004	6	1	5	0	108
ASE_00402	RNaseP_bact_a links to Rfam database...	0.46	0.27	0.79	23	42457	6	1	5	0	62
ASE_00403	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.79	23	55916	6	1	5	0	84
ASE_00404	RNaseP_bact_a links to Rfam database...	0.46	0.27	0.79	23	43042	6	1	5	0	62
ASE_00406	RNaseP_bact_a links to Rfam database...	0.44	0.24	0.79	23	48799	6	1	5	0	71
ASE_00411	RNaseP_bact_a links to Rfam database...	0.41	0.25	0.69	22	49423	10	5	5	0	67
ASE_00412	RNaseP_bact_a links to Rfam database...	0.39	0.21	0.73	22	58281	8	3	5	0	83
ASE_00413	RNaseP_bact_a links to Rfam database...	0.46	0.27	0.79	22	44523	6	1	5	0	59
ASE_00414	RNaseP_bact_a links to Rfam database...	0.42	0.24	0.74	23	46329	8	3	5	0	72
ASE_00415	RNaseP_bact_a links to Rfam database...	0.33	0.17	0.68	17	54921	8	1	7	0	86
ASE_00416	RNaseP_bact_a links to Rfam database...	0.47	0.28	0.80	35	77377	9	1	8	0	92
ASE_00417	RNaseP_arch links to Rfam database...	0.76	0.59	0.98	59	54555	1	0	1	0	41
ASE_00418	RNaseP_arch links to Rfam database...	0.77	0.60	0.98	45	38735	1	0	1	0	30
ASE_00419	RNaseP_bact_a links to Rfam database...	0.40	0.21	0.73	22	54916	8	2	6	0	81
ASE_00422	RNaseP_bact_a links to Rfam database...	0.40	0.19	0.86	18	46950	3	0	3	0	76
ASE_00423	RNaseP_bact_a links to Rfam database...	0.51	0.32	0.81	35	56910	8	1	7	0	74
ASE_00426	RNaseP_bact_a links to Rfam database...	0.25	0.13	0.48	14	61046	15	1	14	0	94
ASE_00428	RNaseP_bact_a links to Rfam database...	0.47	0.28	0.80	35	76592	9	1	8	0	90
ASE_00430	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.83	20	46947	4	0	4	0	77
ASE_00431	RNaseP_bact_a links to Rfam database...	0.38	0.23	0.63	22	46325	13	3	10	0	73
ASE_00434	RNaseP_bact_b links to Rfam database...	0.64	0.50	0.82	55	68198	17	1	11	5	55
ASE_00437	RNaseP_bact_a links to Rfam database...	0.30	0.17	0.55	23	79359	19	1	18	0	112
ASE_00438	RNaseP_bact_a links to Rfam database...	0.39	0.20	0.77	23	66036	7	2	5	0	93
ASE_00441	RNaseP_bact_a links to Rfam database...	0.38	0.19	0.78	21	64234	7	1	5	1	91
ASE_00447	RNaseP_bact_a links to Rfam database...	0.50	0.31	0.82	36	60334	8	1	7	0	80
ASE_00448	RNaseP_bact_a links to Rfam database...	0.48	0.30	0.77	34	64217	10	1	9	0	78
ASE_00451	RNaseP_bact_a links to Rfam database...	0.48	0.29	0.82	36	70832	8	1	7	0	89
CRW_00013	Intron_gpI links to Rfam database...	0.46	0.23	0.90	27	103710	3	0	3	0	88
CRW_00016	Intron_gpI links to Rfam database...	0.45	0.23	0.90	27	77391	3	0	3	0	93
CRW_00610	Intron_gpI links to Rfam database...	0.54	0.31	0.96	25	36289	3	0	1	2	56
CRW_00613	Intron_gpI links to Rfam database...	0.42	0.22	0.81	17	34959	6	0	4	2	61
CRW_00614	Intron_gpI links to Rfam database...	0.45	0.32	0.64	18	121743	11	2	8	1	39
CRW_00618	Intron_gpI links to Rfam database...	0.39	0.26	0.59	16	56253	11	2	9	0	45
CRW_00619	Intron_gpI links to Rfam database...	0.41	0.23	0.74	17	165002	7	0	6	1	56
CRW_00620	Intron_gpI links to Rfam database...	0.35	0.21	0.59	13	150953	16	0	9	7	50
CRW_00621	Intron_gpI links to Rfam database...	0.36	0.21	0.60	15	153156	11	2	8	1	56
CRW_00623	Intron_gpI links to Rfam database...	0.35	0.18	0.68	15	129773	9	1	6	2	68
CRW_00633	Intron_gpI links to Rfam database...	0.40	0.21	0.76	22	63517	7	2	5	0	84
CRW_00634	Intron_gpI links to Rfam database...	0.37	0.18	0.74	17	64597	12	0	6	6	77
CRW_00670	Intron_gpI links to Rfam database...	0.48	0.24	0.97	29	70095	1	0	1	0	91
CRW_00671	Intron_gpI links to Rfam database...	0.49	0.25	0.97	29	62805	1	0	1	0	88
CRW_00672	Intron_gpI links to Rfam database...	0.50	0.26	0.97	29	72360	1	0	1	0	82
CRW_00674	Intron_gpI links to Rfam database...	0.29	0.14	0.63	17	83409	10	6	4	0	107
CRW_00676	Intron_gpI links to Rfam database...	0.32	0.15	0.68	17	93503	13	0	8	5	98
CRW_00692	Intron_gpI links to Rfam database...	0.34	0.17	0.68	15	68613	13	0	7	6	75
PDB_00827	Intron_gpI links to Rfam database...	0.35	0.21	0.59	17	26999	12	2	10	0	64
PDB_00919	RNaseP_bact_a links to Rfam database...	0.33	0.18	0.58	19	44220	16	1	13	2	84
RFA_00597	Telomerase-vert links to Rfam database...	0.71	0.61	0.84	66	97824	18	0	13	5	43
RFA_00598	Telomerase-vert links to Rfam database...	0.68	0.58	0.79	59	84591	25	0	16	9	42
RFA_00599	Telomerase-vert links to Rfam database...	0.79	0.66	0.95	73	101398	7	0	4	3	38
RFA_00600	Telomerase-vert links to Rfam database...	0.76	0.63	0.91	63	120226	15	0	6	9	37
RFA_00601	Telomerase-vert links to Rfam database...	0.79	0.67	0.93	76	99153	10	0	6	4	38
RFA_00602	Telomerase-vert links to Rfam database...	0.76	0.65	0.90	75	101392	11	0	8	3	41
TMR_00173	tmRNA links to Rfam database...	0.19	0.07	0.50	3	42189	9	0	3	6	39
TMR_00357	tmRNA links to Rfam database...	0.30	0.16	0.56	15	83001	12	3	9	0	77
TMR_00601	tmRNA links to Rfam database...	0.53	0.29	1.00	12	58984	9	0	0	9	30
TMR_00696	tmRNA links to Rfam database...	0.28	0.14	0.55	16	85049	13	0	13	0	98

^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 PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

2. Individual counts for PknotsRG [ download as .csv ]

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

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

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