Schema for GlimmerHMM Genes (BUSCO) - GlimmerHMM Gene Predictions with BUSCO Training Set

Database: DobsGB1 Primary Table: glimmerBUSCO Row Count: 7,243 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	BDQP01000001.path1.gene1	`varchar(255)`	values
`chrom`	BDQP01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	9454	`int(10) unsigned`	range
`txEnd`	34605	`int(10) unsigned`	range
`cdsStart`	9454	`int(10) unsigned`	range
`cdsEnd`	34605	`int(10) unsigned`	range
`exonCount`	13	`int(10) unsigned`	range
`exonStarts`	9454,15356,18970,23346,2591...	`longblob`
`exonEnds`	9510,15385,19158,23987,2604...	`longblob`
`score`	0	`int(11)`	range
`name2`	BDQP01000001.path1.gene1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,2,1,0,2,1,0,1,1,1,0,0,1,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	BDQP01000001.path1.gene1	BDQP01000001	+	9454	34605	9454	34605	13	9454,15356,18970,23346,25913,26185,26487,27912,30315,30773,31448,34316,34588,	9510,15385,19158,23987,26047,26361,26722,28683,30687,31387,32084,34461,34605,	BDQP01000001.path1.gene1	unk	unk	0,2,1,0,2,1,0,1,1,1,0,0,1,
585	BDQP01000001.path1.gene2	BDQP01000001	-	37921	61925	37921	61925	19	37921,38186,38378,38594,40149,40864,43483,43884,46084,46501,46772,46886,47177,49733,49970,50335,50566,51679,61875,	38092,38315,38536,38701,40805,41081,43812,44037,46428,46695,46821,47100,47350,49898,50265,50488,51616,51869,61925,	BDQP01000001.path1.gene2	unk	unk	0,0,1,2,0,2,0,0,1,2,1,0,1,1,0,0,0,2,0,
585	BDQP01000001.path1.gene3	BDQP01000001	+	65032	76079	65032	76079	6	65032,71112,73000,73214,74877,75646,	65079,71128,73141,73955,74987,76079,	BDQP01000001.path1.gene3	unk	unk	0,2,0,0,0,2,
585	BDQP01000001.path1.gene4	BDQP01000001	+	78088	79690	78088	79690	3	78088,78665,79350,	78594,79283,79690,	BDQP01000001.path1.gene4	unk	unk	0,2,2,
585	BDQP01000001.path1.gene5	BDQP01000001	-	80906	85756	80906	85756	10	80906,81340,82732,83244,83591,84480,84855,85127,85499,85712,	80915,82670,83181,83534,83811,84795,85067,85437,85647,85756,	BDQP01000001.path1.gene5	unk	unk	0,2,0,1,0,0,1,0,2,0,
585	BDQP01000001.path1.gene6	BDQP01000001	+	86989	95768	86989	95768	8	86989,89485,90077,90376,91452,94421,95482,95673,	87780,89999,90278,90526,91541,94447,95650,95768,	BDQP01000001.path1.gene6	unk	unk	0,2,0,0,0,2,1,1,
585	BDQP01000001.path1.gene7	BDQP01000001	-	96962	109602	96962	109602	6	96962,102289,107130,108781,108930,109433,	97315,102405,107506,108874,109098,109602,	BDQP01000001.path1.gene7	unk	unk	1,2,1,1,1,0,
585	BDQP01000001.path1.gene8	BDQP01000001	+	111463	112574	111463	112574	2	111463,111863,	111475,112574,	BDQP01000001.path1.gene8	unk	unk	0,0,
585	BDQP01000001.path1.gene9	BDQP01000001	+	115104	119266	115104	119266	4	115104,118219,118557,118986,	115115,118493,118628,119266,	BDQP01000001.path1.gene9	unk	unk	0,2,0,2,
585	BDQP01000001.path1.gene10	BDQP01000001	-	120708	126986	120708	126986	5	120708,123154,123756,124187,126980,	121502,123364,124111,124493,126986,	BDQP01000001.path1.gene10	unk	unk	1,1,0,0,0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

GlimmerHMM Genes (BUSCO) (glimmerBUSCO) Track Description


	Description This track shows the gene predictions from the GlimmerHMM gene finder using the species-specific parameters estimated from a training set produced by BUSCO. Methods The training set used to estimate the species-specific parameters for the GlimmerHMM analysis was produced by BUSCO using the arthropoda_odb9 dataset. References Majoros WH, Pertea M, Salzberg SL. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics. 2004 Nov 1;20(16):2878-9. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015 Oct 1;31(19):3210-2.

Description

Methods

References