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

Database: DvirCAF1 Primary Table: glimmerBUSCO Row Count: 5,577 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_10051.path1.gene1	`varchar(255)`	values
`chrom`	scaffold_10051	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	538	`int(10) unsigned`	range
`txEnd`	685	`int(10) unsigned`	range
`cdsStart`	538	`int(10) unsigned`	range
`cdsEnd`	685	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	538,	`longblob`
`exonEnds`	685,	`longblob`
`score`	0	`int(11)`	range
`name2`	scaffold_10051.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_10051.path1.gene1	scaffold_10051	-	538	685	538	685	1	538,	685,	scaffold_10051.path1.gene1	unk	unk	0,
585	scaffold_10171.path1.gene1	scaffold_10171	+	608	632	608	632	1	608,	632,	scaffold_10171.path1.gene1	unk	unk	0,
585	scaffold_10248.path1.gene1	scaffold_10248	+	500	854	500	854	1	500,	854,	scaffold_10248.path1.gene1	unk	unk	0,
585	scaffold_10277.path1.gene1	scaffold_10277	-	2647	2723	2647	2723	1	2647,	2723,	scaffold_10277.path1.gene1	unk	unk	2,
585	scaffold_10322.path1.gene1	scaffold_10322	-	40663	40786	40663	40786	1	40663,	40786,	scaffold_10322.path1.gene1	unk	unk	0,
585	scaffold_10322.path1.gene2	scaffold_10322	-	48993	63856	48993	63856	6	48993,59799,62541,62670,63414,63710,	49001,61330,62607,62887,63642,63856,	scaffold_10322.path1.gene2	unk	unk	1,0,0,2,2,0,
585	scaffold_10322.path1.gene3	scaffold_10322	+	67608	69166	67608	69166	4	67608,67750,67907,68687,	67692,67848,68632,69166,	scaffold_10322.path1.gene3	unk	unk	0,0,2,1,
585	scaffold_10322.path1.gene4	scaffold_10322	+	76569	88110	76569	88110	6	76569,81312,82713,84693,86290,88086,	80559,81390,84637,85297,86891,88110,	scaffold_10322.path1.gene4	unk	unk	0,0,0,1,2,0,
585	scaffold_10322.path1.gene5	scaffold_10322	+	91256	94920	91256	94920	5	91256,92250,92644,92807,94911,	91782,92583,92748,93587,94920,	scaffold_10322.path1.gene5	unk	unk	0,1,1,0,0,
585	scaffold_10322.path1.gene6	scaffold_10322	+	95577	123126	95577	123126	9	95577,97047,97278,100008,100678,101818,105658,106045,123120,	96992,97228,99948,100323,101755,105596,105978,107233,123126,	scaffold_10322.path1.gene6	unk	unk	0,2,0,0,0,0,1,0,0,

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