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

Database: DyakCAF1 Primary Table: glimmerBUSCO Row Count: 6,103 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	chr2L.path1.gene1	`varchar(255)`	values
`chrom`	chr2L	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	10856	`int(10) unsigned`	range
`txEnd`	11465	`int(10) unsigned`	range
`cdsStart`	10856	`int(10) unsigned`	range
`cdsEnd`	11465	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	10856,	`longblob`
`exonEnds`	11465,	`longblob`
`score`	0	`int(11)`	range
`name2`	chr2L.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	chr2L.path1.gene1	chr2L	-	10856	11465	10856	11465	1	10856,	11465,	chr2L.path1.gene1	unk	unk	0,
585	chr2L.path1.gene2	chr2L	-	20962	69701	20962	69701	10	20962,21194,21490,22503,27591,28097,28211,32040,32502,69577,	21130,21393,21928,22729,27815,28144,28695,32237,33059,69701,	chr2L.path1.gene2	unk	unk	0,2,2,1,2,0,2,0,1,0,
585	chr2L.path1.gene3	chr2L	-	72463	88112	72463	88112	2	72463,88099,	73485,88112,	chr2L.path1.gene3	unk	unk	1,0,
585	chr2L.path1.gene4	chr2L	+	89340	93602	89340	93602	5	89340,90594,92369,92835,93559,	89862,90889,92798,92908,93602,	chr2L.path1.gene4	unk	unk	0,0,1,1,2,
585	chr2L.path1.gene5	chr2L	-	93839	94480	93839	94480	2	93839,94370,	94314,94480,	chr2L.path1.gene5	unk	unk	2,0,
585	chr2L.path1.gene6	chr2L	+	98063	102984	98063	102984	6	98063,99782,99927,100177,101876,102965,	98187,99860,100050,100290,102556,102984,	chr2L.path1.gene6	unk	unk	0,1,1,1,0,2,
585	chr2L.path1.gene7	chr2L	-	106326	114200	106326	114200	5	106326,107256,107656,113092,114038,	106355,107600,107802,113926,114200,	chr2L.path1.gene7	unk	unk	1,2,0,0,0,
585	chr2L.path1.gene8	chr2L	-	115113	119787	115113	119787	3	115113,117921,119743,	115235,118064,119787,	chr2L.path1.gene8	unk	unk	1,2,0,
585	chr2L.path1.gene9	chr2L	+	121776	122976	121776	122976	1	121776,	122976,	chr2L.path1.gene9	unk	unk	0,
73	chr2L.path1.gene10	chr2L	-	127595	141632	127595	141632	9	127595,128005,130504,130779,132824,134206,137690,138231,140429,	127606,128282,130551,131682,133014,135242,138178,138579,141632,	chr2L.path1.gene10	unk	unk	1,0,1,1,0,2,0,0,0,

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