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

Database: DpseGB3 Primary Table: glimmerBUSCO Row Count: 5,555 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CH379058.path1.gene1	`varchar(255)`	values
`chrom`	CH379058	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	17139	`int(10) unsigned`	range
`txEnd`	22628	`int(10) unsigned`	range
`cdsStart`	17139	`int(10) unsigned`	range
`cdsEnd`	22628	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	17139,	`longblob`
`exonEnds`	22628,	`longblob`
`score`	0	`int(11)`	range
`name2`	CH379058.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	CH379058.path1.gene1	CH379058	-	17139	22628	17139	22628	1	17139,	22628,	CH379058.path1.gene1	unk	unk	0,
585	CH379058.path1.gene2	CH379058	-	57590	64766	57590	64766	2	57590,61770,	57723,64766,	CH379058.path1.gene2	unk	unk	2,0,
585	CH379058.path1.gene3	CH379058	+	68693	69631	68693	69631	2	68693,69530,	69471,69631,	CH379058.path1.gene3	unk	unk	0,1,
585	CH379058.path1.gene4	CH379058	-	70546	71053	70546	71053	1	70546,	71053,	CH379058.path1.gene4	unk	unk	0,
585	CH379058.path1.gene5	CH379058	-	74330	78389	74330	78389	6	74330,74559,75375,75584,75859,78100,	74417,74715,75522,75770,76029,78389,	CH379058.path1.gene5	unk	unk	0,0,0,0,1,0,
73	CH379058.path1.gene6	CH379058	-	125772	156324	125772	156324	2	125772,154286,	125825,156324,	CH379058.path1.gene6	unk	unk	1,0,
586	CH379058.path1.gene7	CH379058	-	156591	159825	156591	159825	3	156591,158199,159633,	156610,159566,159825,	CH379058.path1.gene7	unk	unk	2,0,0,
586	CH379058.path1.gene8	CH379058	-	162201	190531	162201	190531	5	162201,189504,189789,189986,190298,	162223,189723,189923,190236,190531,	CH379058.path1.gene8	unk	unk	2,2,0,2,0,
586	CH379058.path1.gene9	CH379058	-	193491	194026	193491	194026	3	193491,193767,193996,	193699,193910,194026,	CH379058.path1.gene9	unk	unk	2,0,0,
586	CH379058.path1.gene10	CH379058	+	195127	202803	195127	202803	5	195127,197724,200957,201351,202619,	195451,198986,201295,202186,202803,	CH379058.path1.gene10	unk	unk	0,0,2,1,2,

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