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

Database: DsimGB2 Primary Table: augustusBUSCO Row Count: 13,290 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CM002910.g1.t1	`varchar(255)`	values
`chrom`	CM002910	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	11595	`int(10) unsigned`	range
`txEnd`	32311	`int(10) unsigned`	range
`cdsStart`	11595	`int(10) unsigned`	range
`cdsEnd`	32311	`int(10) unsigned`	range
`exonCount`	13	`int(10) unsigned`	range
`exonStarts`	11595,13505,14010,14238,159...	`longblob`
`exonEnds`	11603,13683,14180,14334,159...	`longblob`
`score`	0	`int(11)`	range
`name2`	CM002910.g1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,0,1,1,2,2,1,0,1,0,0,1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	CM002910.g1.t1	CM002910	-	11595	32311	11595	32311	13	11595,13505,14010,14238,15939,18260,19067,22919,25519,26233,27524,30754,32295,	11603,13683,14180,14334,15953,18698,19293,23106,25770,26660,29318,31311,32311,	CM002910.g1	unk	unk	1,0,1,1,2,2,1,0,1,0,0,1,0,
585	CM002910.g2.t1	CM002910	+	56097	59699	56097	59699	3	56097,58364,59606,	56360,58740,59699,	CM002910.g2	unk	unk	0,2,0,
585	CM002910.g3.t1	CM002910	+	87202	89866	87202	89866	5	87202,87659,88692,89109,89618,	87256,87681,89010,89538,89866,	CM002910.g3	unk	unk	0,0,1,1,1,
585	CM002910.g4.t1	CM002910	-	90558	92731	90558	92731	6	90558,91090,91360,91476,91596,92192,	91033,91123,91422,91541,92000,92731,	CM002910.g4	unk	unk	2,2,0,1,2,0,
585	CM002910.g5.t1	CM002910	+	94798	99635	94798	99635	6	94798,96473,96808,97058,98782,99526,	94922,96551,96931,97228,99462,99635,	CM002910.g5	unk	unk	0,1,1,1,0,2,
585	CM002910.g6.t1	CM002910	-	101745	104500	101745	104500	4	101745,103577,103802,104372,	102140,103746,104316,104500,	CM002910.g6	unk	unk	1,0,2,0,
585	CM002910.g7.t1	CM002910	-	108730	114693	108730	114693	7	108730,109307,109469,109700,110714,111754,114509,	109114,109408,109638,110534,110904,111872,114693,	CM002910.g7	unk	unk	0,1,0,0,2,1,0,
585	CM002910.g8.t1	CM002910	+	118230	119430	118230	119430	1	118230,	119430,	CM002910.g8	unk	unk	0,
585	CM002910.g9.t1	CM002910	-	124238	124957	124238	124957	3	124238,124360,124876,	124244,124819,124957,	CM002910.g9	unk	unk	0,0,0,
585	CM002910.g10.t1	CM002910	-	125092	128112	125092	128112	6	125092,125366,125739,126882,127020,127295,	125309,125580,126495,126965,127234,128112,	CM002910.g10	unk	unk	2,1,1,2,1,0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Augustus Genes (BUSCO) (augustusBUSCO) Track Description


	Description This track shows the gene models from the Augustus gene predictor 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 Augustus analysis was produced by BUSCO using the arthropoda_odb9 dataset. Transposons remnants identified by RepeatMasker were provided as hints to the Augustus gene predictor. The following additional parameters were used with the Augustus gene predictor: --strand=both --noInFrameStop=true --gff3=on --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --cds=on --singlestrand=false --UTR=off --genemodel=partial References Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25. 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