Considerations in the identification of functional RNA structural elements in genomic alignments

Babak, Tomas; Blencowe, Benjamin J; Hughes, Timothy R

doi:10.1186/1471-2105-8-33

BMC Bioinformatics

Table 2 Details of results on test set, tabulated at 15%, 50%, and 85% overall recall

From: Considerations in the identification of functional RNA structural elements in genomic alignments

		15% overall recall			50% overall recall			85% overall recall
	Sample size	Proportion positive	Number positive	Precision	Proportion positive	Number positive	Precision	Proportion positive	Number positive	Precision
RNAz
miRNA	1303	0.208	271	0.158	0.743	968	0.070	0.992	1293	0.017
tRNA	213	0.099	21	0.103	0.723	154	0.078	0.981	209	0.016
snRNA	227	0.141	32	0.375	0.379	86	0.071	0.846	192	0.014
Box H/ACA snoRNA	222	0.252	56	0.356	0.541	120	0.094	0.887	197	0.018
Box C/D snoRNA	573	0.012	7	0.029	0.092	53	0.029	0.625	358	0.013
Regulatory	181	0.293	53	0.047	0.431	78	0.045	0.823	149	0.019
Other	94	0.117	11	0.538	0.362	34	0.042	0.777	73	0.011
Non-structural	215	0.023	5	0.049	0.102	22	0.029	0.484	104	0.012
All	3029	0.151	456	0.123	0.500	1515	0.064	0.850	2576	0.016
Negatives – shuffle-pair	300399	0.011	3216	NA	0.071	21315	NA	0.585	175584	NA
Negatives – shuffle-aln	299784	0.001	407	NA	0.023	7044	NA	0.595	178278	NA
QRNA
miRNA	1303	0.293	382	0.065	0.802	1045	0.069	0.972	1267	0.029
tRNA	213	0.103	22	0.030	0.803	171	0.039	0.911	194	0.023
snRNA	227	0.070	16	0.009	0.278	63	0.022	0.797	181	0.014
Box H/ACA snoRNA	222	0.023	5	0.023	0.194	43	0.020	0.829	184	0.017
Box C/D snoRNA	573	0.012	7	0.004	0.143	82	0.027	0.705	404	0.025
Regulatory	181	0.039	7	0.020	0.337	61	0.038	0.878	159	0.028
Other	94	0.064	6	0.011	0.255	24	0.019	0.798	75	0.016
Non-structural	215	0.047	10	0.004	0.126	27	0.008	0.516	111	0.018
All	3029	0.150	455	0.037	0.501	1516	0.048	0.850	2576	0.025
Negatives – shuffle-pair	302377	0.035	10452	NA	0.117	35389	NA	0.493	149137	NA
Negatives – shuffle-aln	299784	0.009	2610	NA	0.038	11463	NA	0.626	187643	NA
ddbRNA
miRNA	1303	0.195	254	0.073	0.800	1042	0.038	0.975	1270	0.011
tRNA	213	0.136	29	0.023	0.901	192	0.032	0.981	209	0.009
snRNA	227	0.141	32	0.049	0.674	153	0.021	0.815	185	0.007
Box H/ACA snoRNA	222	0.243	54	0.081	0.644	143	0.020	0.838	186	0.010
Box C/D snoRNA	573	0.044	25	0.018	0.356	204	0.013	0.660	378	0.006
Regulatory	181	0.210	38	0.034	0.641	116	0.022	0.796	144	0.008
Other	94	0.128	12	0.032	0.649	61	0.016	0.787	74	0.007
Non-structural	215	0.051	11	0.009	0.363	78	0.009	0.628	135	0.007
All	3029	0.150	455	0.046	0.657	1990	0.025	0.852	2582	0.009
Negatives – shuffle-pair	303277	0.031	9251	NA	0.607	183998	NA	0.921	279240	NA
Negatives – shuffle-aln	299784	0.012	3546	NA	0.363	108707	NA	0.620	185895	NA
Evofold
miRNA	1303	0.324	422	0.243	0.836	1089	0.044	0.968	1261	0.018
tRNA	213	0.009	2	0.000	0.601	128	0.026	0.953	203	0.014
snRNA	227	0.101	23	0.409	0.370	84	0.017	0.811	184	0.013
Box H/ACA snoRNA	222	0.009	2	0.333	0.297	66	0.074	0.671	149	0.032
Box C/D snoRNA	573	0.002	1	0.500	0.082	47	0.018	0.757	434	0.011
Regulatory	181	0.006	1	0.000	0.210	38	0.040	0.939	170	0.012
Other	94	0.000	0	0.000	0.213	20	0.027	0.543	51	0.018
Non-structural	215	0.019	4	0.056	0.195	42	0.027	0.591	127	0.016
All	3029	0.150	455	0.240	0.500	1515	0.038	0.852	2580	0.017
Negatives – shuffle-pair	304600	0.013	3809	NA	0.199	60544	NA	0.768	234058	NA
Negatives – shuffle-aln	299784	0.010	3115	NA	0.151	45175	NA	0.773	231828	NA
Alifoldz
miRNA	1290	0.307	396	0.916	0.650	838	0.055	0.940	1213	0.016
tRNA	201	0.010	2	0.091	0.731	147	0.046	0.995	200	0.013
snRNA	226	0.009	2	0.667	0.416	94	0.048	0.925	209	0.013
Box H/ACA snoRNA	219	0.018	4	1.000	0.493	108	0.043	0.932	204	0.018
Box C/D snoRNA	543	0.009	5	0.667	0.210	114	0.026	0.727	395	0.010
Regulatory	175	0.154	27	0.043	0.537	94	0.034	0.943	165	0.018
Other	92	0.033	3	1.000	0.207	19	0.058	0.848	78	0.013
Non-structural	198	0.025	5	0.833	0.298	59	0.020	0.717	142	0.011
All	2945	0.151	444	0.369	0.500	1473	0.045	0.885	2607	0.014
Negatives – shuffle-pair	290247	0.003	778	NA	0.145	42219	NA	0.558	161948	NA
Negatives – shuffle-aln	299784	0.000	74	NA	0.499	149651	NA	0.761	228278	NA
zRNAfold (Dual)
miRNA	1303	0.347	452	0.987	0.927	1208	0.399	0.992	1293	0.024
tRNA	213	0.000	0	0.000	0.221	47	0.065	0.981	209	0.020
snRNA	227	0.004	1	0.000	0.291	66	0.139	0.802	182	0.018
Box H/ACA snoRNA	222	0.000	0	0.000	0.311	69	0.286	0.883	196	0.026
Box C/D snoRNA	573	0.000	0	0.000	0.045	26	0.029	0.642	368	0.017
Regulatory	181	0.006	1	0.000	0.354	64	0.056	0.895	162	0.019
Other	94	0.000	0	0.000	0.255	24	0.112	0.755	71	0.015
Non-structural	215	0.005	1	1.000	0.051	11	0.139	0.433	93	0.015
All	3029	0.150	455	0.746	0.500	1515	0.249	0.850	2575	0.021
Negatives – shuffle-pair	301496	0.000	150	NA	0.019	5859	NA	0.454	136915	NA
Negatives – shuffle-aln	299784	0.000	27	NA	0.015	4530	NA	0.421	126347	NA
zRNAfold
miRNA	1303	0.345	450	0.968	0.912	1188	0.339	0.992	1292	0.022
tRNA	213	0.000	0	0.000	0.225	48	0.068	1.000	213	0.019
snRNA	227	0.009	2	0.000	0.273	62	0.148	0.811	184	0.017
Box H/ACA snoRNA	222	0.000	0	0.000	0.365	81	0.213	0.883	196	0.022
Box C/D snoRNA	573	0.002	1	0.500	0.075	43	0.031	0.620	355	0.014
Regulatory	181	0.000	0	0.000	0.331	60	0.051	0.845	153	0.018
Other	94	0.011	1	1.000	0.234	22	0.080	0.766	72	0.016
Non-structural	215	0.009	2	1.000	0.056	12	0.047	0.507	109	0.015
All	3029	0.151	456	0.806	0.501	1516	0.201	0.850	2575	0.019
Negatives – shuffle-pair	302578	0.000	143	NA	0.024	7292	NA	0.484	146426	NA
Negatives – shuffle-aln	299784	0.000	27	NA	0.020	5958	NA	0.484	145172	NA
zMFOLD
miRNA	1303	0.342	446	0.943	0.906	1181	0.162	0.992	1293	0.023
tRNA	213	0.000	0	0.000	0.075	16	0.016	0.995	212	0.019
snRNA	227	0.000	0	0.000	0.242	55	0.059	0.802	182	0.015
Box H/ACA snoRNA	222	0.000	0	0.000	0.486	108	0.101	0.919	204	0.020
Box C/D snoRNA	573	0.002	1	0.167	0.072	41	0.014	0.593	340	0.012
Regulatory	181	0.022	4	0.017	0.365	66	0.034	0.812	147	0.016
Other	94	0.021	2	1.000	0.245	23	0.051	0.723	68	0.013
Non-structural	215	0.009	2	0.400	0.116	25	0.026	0.595	128	0.012
All	3029	0.150	455	0.675	0.500	1515	0.093	0.850	2575	0.018
Negatives – shuffle-pair	302950	0.001	241	NA	0.054	16498	NA	0.515	156071	NA
Negatives – shuffle-aln	299784	0.000	39	NA	0.042	12716	NA	0.522	156435	NA

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