Computational discovery and annotation of conserved small open reading frames in fungal genomes

Mat-Sharani, Shuhaila; Firdaus-Raih, Mohd

doi:10.1186/s12859-018-2550-2

BMC Bioinformatics

Table 1 List of sORFs predicted from the whole genome and intergenic regions of fungal genomes

From: Computational discovery and annotation of conserved small open reading frames in fungal genomes

Microorganisms (yeast/fungi)	Phylum	Genome size (Mb)	Scaffolds(sc)/ Chromosomes	Intergenic region	Intron	ORF	sORFs from genome annotation	sORF from ab initio prediction						Total sORFs predicted
								GetORF		sORFfinder	Combined 1st & 2nd approached	sORFs match ORF homolog	sORFs ab initio predicted
								Genome	Intergenic	sORFfinder	Combined 1st & 2nd approached	sORFs match ORF homolog	sORFs ab initio predicted
Agaricus bisporus	Basidiomycetes	30.78	29sc	10,606	50,859	10,450	575	423,332	113,990	902,110	2808	1952	856	1431
Aspergillus fumigatus	Ascomycetes	29.39	16	9916	18,630	9630	180	329,750	644,099	746,886	6665	5212	1453	1633
Aspergillus nidulans	Ascomycetes	29.83	17	9410	25,192	9410	83	376,689	533,546	288,159	3031	1803	1228	1311
Aspergillus niger	Ascomycetes	38.50	20sc	10,828	25,160	10,609	90	454,556	645,989	431,379	2950	1690	1260	1350
Aspergillus oryzae	Ascomycetes	37.91	27sc	12,937	29,686	12,818	172	508,537	639,035	361,674	3336	2042	1294	1466
Candida dubliniensis	Ascomycetes	14.62	8	5499	169	5213	45	180,147	249,542	181,108	4591	2046	2545	2590
Candida glabrata	Ascomycetes	12.34	14	6580	33,084	6575	159	153,883	203,269	290,815	2593	1271	1322	1481
Cryptococcus gattii	Basidiomycetes	18.37	14	6617	34,336	6475	94	250,564	331,357	263,216	2447	1864	583	677
Cryptococcus neoformans	Basidiomycetes	2.50	14	6658	479	6290	110	254,930	329,135	247,268	2266	1673	593	703
Debaryomyces hansenii	Ascomycetes	2.25	8	2029	32	1996	300	153,782	190,959	165,774	4179	2540	1639	1939
Encephalitozoon cuniculi	Microsporidia	2.22	11	1892	14	1833	13	28,102	33,715	53,062	554	396	158	171
Encephalitozoon intestinalis	Microsporidia	2.19	11	4853	239	4434	18	26,156	28,950	54,302	543	412	131	149
Eremothecium cymbalariae	Microsporidia	9.67	8	5356	276	4776	61	119,153	153,876	171,154	3384	1865	1519	1580
Eremothecium gossypii	Microsporidia	9.12	8	11,624	25,808	11,628	80	94,967	117,788	121,934	3529	2265	1264	1344
Gibberella zeae	Ascomycetes	38.05	11	5649	1040	5378	104	488,905	698,951	151,211	4487	2265	1832	1936
Kazachstania africana	Ascomycetes	11.13	12	5649	1040	5378	88	144,748	186,855	141,681	1894	1247	647	735
Kluyveromyces lactis	Ascomycetes	10.73	7	5412	182	5085	73	139,746	182,755	81,044	3006	1636	1370	1443
Lachancea thermotolerans	Ascomycetes	10.39	8	5498	284	5091	53	114,598	145,278	155,291	3134	1628	1506	1559
Magnaporthe grisea	Ascomycetes	40.30	8	14,210	25,265	14,014	1105	506,420	699,033	217,609	4466	2735	1731	2836
Myceliophthora thermophila	Ascomycetes	38.74	7	9294	15,500	9099	419	343,719	540,155	140,855	4738	2547	2191	2610
Naumovozyma castellii	Ascomycetes	11.22	10	5870	203	5592	102	147,551	187,871	187,462	5691	3430	2261	2363
Naumovozyma dairenensis	Ascomycetes	13.53	12	6057	177	5772	99	185,531	251,917	231,996	2841	1323	1518	1617
Pichia pastoris	Ascomycetes	9.60	4	5040	578	5040	89	112,299	138,917	61,604	4161	2872	1289	1378
Pichia stipitis	Ascomycetes	15.44	8	5816	2567	5816	61	186,356	259,185	79,673	2146	1008	1138	1199
Saccharomyces cerevisiae	Ascomycetes	12.16	17	6349	366	5906	224	153,187	200,252	398,979	3478	2196	1282	1506
Schizosaccharomyces pombe	Ascomycetes	12.59	4	6991	3793	5133	124	165,857	165,864	33,542	6027	3304	2723	2847
Tetrapisispora phaffii	Ascomycetes	12.12	16	5460	141	5250	89	153,895	206,397	825,322	2959	1410	1549	1638
Thielavia terrestris	Ascomycetes	36.91	6	9958	17,290	9802	72	296,185	443,166	163,032	3291	1966	1325	1397
Torulaspora delbrueckii	Ascomycetes	9.22	8	5176	203	4972	402	113,250	138,118	509,930	4521	3074	1447	1849
Yarrowia lipolytica	Ascomycetes	20.55	7	7357	1120	6472	106	242,726	369,856	127,236	1594	456	1138	1244
Zygosaccharomyces rouxii	Ascomycetes	9.76	7	5332	166	4991	65	123,372	154,232	353,232	4429	2634	1795	1860
TOTAL						210,928	5255	6,972,893	9,184,052	902,110	105,739		42,587	47,842

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ISSN: 1471-2105

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