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

Database: DmojCAF1 Primary Table: glimmerBUSCO Row Count: 5,987 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_1245.path1.gene1	`varchar(255)`	values
`chrom`	scaffold_1245	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	778	`int(10) unsigned`	range
`txEnd`	934	`int(10) unsigned`	range
`cdsStart`	778	`int(10) unsigned`	range
`cdsEnd`	934	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	778,	`longblob`
`exonEnds`	934,	`longblob`
`score`	0	`int(11)`	range
`name2`	scaffold_1245.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	scaffold_1245.path1.gene1	scaffold_1245	+	778	934	778	934	1	778,	934,	scaffold_1245.path1.gene1	unk	unk	0,
585	scaffold_1311.path1.gene1	scaffold_1311	-	1056	1426	1056	1426	1	1056,	1426,	scaffold_1311.path1.gene1	unk	unk	2,
585	scaffold_1392.path1.gene1	scaffold_1392	+	1275	1518	1275	1518	1	1275,	1518,	scaffold_1392.path1.gene1	unk	unk	0,
585	scaffold_1420.path1.gene1	scaffold_1420	+	72	1600	72	1600	2	72,1207,	708,1600,	scaffold_1420.path1.gene1	unk	unk	0,0,
585	scaffold_1435.path1.gene1	scaffold_1435	-	457	489	457	489	1	457,	489,	scaffold_1435.path1.gene1	unk	unk	1,
585	scaffold_1444.path1.gene1	scaffold_1444	+	1072	1102	1072	1102	1	1072,	1102,	scaffold_1444.path1.gene1	unk	unk	0,
585	scaffold_1488.path1.gene1	scaffold_1488	-	914	970	914	970	1	914,	970,	scaffold_1488.path1.gene1	unk	unk	1,
585	scaffold_1504.path1.gene1	scaffold_1504	-	801	867	801	867	1	801,	867,	scaffold_1504.path1.gene1	unk	unk	0,
585	scaffold_1511.path1.gene1	scaffold_1511	-	656	751	656	751	1	656,	751,	scaffold_1511.path1.gene1	unk	unk	0,
585	scaffold_1526.path1.gene1	scaffold_1526	-	43	196	43	196	1	43,	196,	scaffold_1526.path1.gene1	unk	unk	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