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

Database: DperCAF1 Primary Table: glimmerBUSCO Row Count: 6,032 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	super_0.path1.gene1	`varchar(255)`	values
`chrom`	super_0	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	25093	`int(10) unsigned`	range
`txEnd`	25135	`int(10) unsigned`	range
`cdsStart`	25093	`int(10) unsigned`	range
`cdsEnd`	25135	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	25093,	`longblob`
`exonEnds`	25135,	`longblob`
`score`	0	`int(11)`	range
`name2`	super_0.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	super_0.path1.gene1	super_0	+	25093	25135	25093	25135	1	25093,	25135,	super_0.path1.gene1	unk	unk	0,
585	super_0.path1.gene2	super_0	-	31930	53673	31930	53673	4	31930,34853,35301,53615,	31946,35075,37345,53673,	super_0.path1.gene2	unk	unk	2,2,1,0,
585	super_0.path1.gene3	super_0	+	55515	68040	55515	68040	4	55515,61860,64016,66008,	55697,62140,65587,68040,	super_0.path1.gene3	unk	unk	0,2,0,2,
585	super_0.path1.gene4	super_0	+	69461	80801	69461	80801	4	69461,71855,79541,79701,	71499,72011,79637,80801,	super_0.path1.gene4	unk	unk	0,1,1,1,
585	super_0.path1.gene5	super_0	-	81885	84050	81885	84050	3	81885,82694,83748,	81961,82952,84050,	super_0.path1.gene5	unk	unk	2,2,0,
585	super_0.path1.gene6	super_0	+	84686	98428	84686	98428	12	84686,85059,85598,86116,86491,86736,86994,89711,92220,94143,95814,98017,	85000,85500,85799,86432,86676,86930,87139,89755,94082,95758,97964,98428,	super_0.path1.gene6	unk	unk	0,2,2,2,0,2,1,2,1,0,1,0,
585	super_0.path1.gene7	super_0	-	100138	103326	100138	103326	3	100138,103025,103275,	100304,103213,103326,	super_0.path1.gene7	unk	unk	2,0,0,
585	super_0.path1.gene8	super_0	+	105663	112214	105663	112214	6	105663,109367,109594,110383,110555,111381,	105820,109537,110321,110484,111327,112214,	super_0.path1.gene8	unk	unk	0,1,0,1,0,1,
585	super_0.path1.gene9	super_0	+	114023	122605	114023	122605	12	114023,114515,114689,117033,117290,117691,120034,120703,121210,121855,122101,122329,	114284,114612,114836,117147,117407,119966,120647,120989,121791,122035,122263,122605,	super_0.path1.gene9	unk	unk	0,0,1,1,1,1,2,0,1,0,0,0,
585	super_0.path1.gene10	super_0	+	124076	126894	124076	126894	9	124076,124521,124842,125252,125494,125725,125931,126227,126763,	124220,124785,125197,125438,125664,125873,126173,126702,126894,	super_0.path1.gene10	unk	unk	0,0,0,1,1,0,1,0,1,

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