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

Database: DhydGB1 Primary Table: glimmerBUSCO Row Count: 6,111 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	NWQH01000001.path1.gene1	`varchar(255)`	values
`chrom`	NWQH01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	23042	`int(10) unsigned`	range
`txEnd`	23050	`int(10) unsigned`	range
`cdsStart`	23042	`int(10) unsigned`	range
`cdsEnd`	23050	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	23042,	`longblob`
`exonEnds`	23050,	`longblob`
`score`	0	`int(11)`	range
`name2`	NWQH01000001.path1.gene1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	NWQH01000001.path1.gene1	NWQH01000001	+	23042	23050	23042	23050	1	23042,	23050,	NWQH01000001.path1.gene1	unk	unk	0,
585	NWQH01000001.path1.gene2	NWQH01000001	+	25994	33679	25994	33679	3	25994,31673,33673,	26000,32153,33679,	NWQH01000001.path1.gene2	unk	unk	0,0,0,
585	NWQH01000001.path1.gene3	NWQH01000001	-	37019	40122	37019	40122	3	37019,38846,39239,	37026,39180,40122,	NWQH01000001.path1.gene3	unk	unk	2,1,0,
585	NWQH01000001.path1.gene4	NWQH01000001	+	40173	64247	40173	64247	4	40173,47178,51164,64143,	40238,47533,51273,64247,	NWQH01000001.path1.gene4	unk	unk	0,2,0,1,
585	NWQH01000001.path1.gene5	NWQH01000001	+	64511	67977	64511	67977	2	64511,67892,	64657,67977,	NWQH01000001.path1.gene5	unk	unk	0,2,
585	NWQH01000001.path1.gene6	NWQH01000001	-	69870	74676	69870	74676	4	69870,73664,73907,74238,	69933,73850,74177,74676,	NWQH01000001.path1.gene6	unk	unk	0,0,0,0,
585	NWQH01000001.path1.gene7	NWQH01000001	+	98015	124469	98015	124469	4	98015,98511,118569,124299,	98438,98632,118674,124469,	NWQH01000001.path1.gene7	unk	unk	0,0,1,1,
586	NWQH01000001.path1.gene8	NWQH01000001	+	131132	168737	131132	168737	10	131132,151306,153874,155978,164199,165479,165974,167383,167896,168720,	131269,151935,153990,156587,164290,165594,166073,167547,168109,168737,	NWQH01000001.path1.gene8	unk	unk	0,2,1,0,0,1,2,2,1,1,
586	NWQH01000001.path1.gene9	NWQH01000001	-	174490	183977	174490	183977	5	174490,181300,181745,182321,183932,	174495,181682,182256,183226,183977,	NWQH01000001.path1.gene9	unk	unk	1,0,2,0,0,
586	NWQH01000001.path1.gene10	NWQH01000001	-	186292	189486	186292	189486	5	186292,186821,187034,188498,189206,	186757,186973,188442,189139,189486,	NWQH01000001.path1.gene10	unk	unk	0,1,0,1,0,

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