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

Database: DanaCAF1 Primary Table: glimmerBUSCO Row Count: 5,478 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_10103.path1.gene1	`varchar(255)`	values
`chrom`	scaffold_10103	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	3136	`int(10) unsigned`	range
`txEnd`	3188	`int(10) unsigned`	range
`cdsStart`	3136	`int(10) unsigned`	range
`cdsEnd`	3188	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	3136,	`longblob`
`exonEnds`	3188,	`longblob`
`score`	0	`int(11)`	range
`name2`	scaffold_10103.path1.gene1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	2,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	scaffold_10103.path1.gene1	scaffold_10103	-	3136	3188	3136	3188	1	3136,	3188,	scaffold_10103.path1.gene1	unk	unk	2,
585	scaffold_10214.path1.gene1	scaffold_10214	-	8831	8968	8831	8968	1	8831,	8968,	scaffold_10214.path1.gene1	unk	unk	1,
585	scaffold_10296.path1.gene1	scaffold_10296	+	265	1246	265	1246	2	265,970,	590,1246,	scaffold_10296.path1.gene1	unk	unk	0,1,
585	scaffold_10376.path1.gene2	scaffold_10376	+	4821	4846	4821	4846	1	4821,	4846,	scaffold_10376.path1.gene2	unk	unk	0,
586	scaffold_10513.path1.gene1	scaffold_10513	+	170347	170455	170347	170455	1	170347,	170455,	scaffold_10513.path1.gene1	unk	unk	0,
585	scaffold_10575.path1.gene1	scaffold_10575	-	726	1053	726	1053	1	726,	1053,	scaffold_10575.path1.gene1	unk	unk	0,
585	scaffold_10575.path1.gene2	scaffold_10575	-	1775	5095	1775	5095	2	1775,4726,	1792,5095,	scaffold_10575.path1.gene2	unk	unk	1,1,
585	scaffold_12101.path1.gene1	scaffold_12101	+	161	199	161	199	1	161,	199,	scaffold_12101.path1.gene1	unk	unk	0,
585	scaffold_12276.path1.gene1	scaffold_12276	+	61114	61127	61114	61127	1	61114,	61127,	scaffold_12276.path1.gene1	unk	unk	0,
585	scaffold_12392.path1.gene1	scaffold_12392	-	35961	35981	35961	35981	1	35961,	35981,	scaffold_12392.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