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

Database: DserGB1 Primary Table: augustusBUSCO Row Count: 14,642 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	MTTC01000001.g1.t1	`varchar(255)`	values
`chrom`	MTTC01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	357	`int(10) unsigned`	range
`txEnd`	7118	`int(10) unsigned`	range
`cdsStart`	357	`int(10) unsigned`	range
`cdsEnd`	7118	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	357,4722,6314,	`longblob`
`exonEnds`	4647,6246,7118,	`longblob`
`score`	0	`int(11)`	range
`name2`	MTTC01000001.g1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	MTTC01000001.g1.t1	MTTC01000001	+	357	7118	357	7118	3	357,4722,6314,	4647,6246,7118,	MTTC01000001.g1	unk	unk	0,0,0,
585	MTTC01000001.g2.t1	MTTC01000001	+	7151	7364	7151	7364	1	7151,	7364,	MTTC01000001.g2	unk	unk	0,
585	MTTC01000001.g3.t1	MTTC01000001	+	7950	8610	7950	8610	2	7950,8438,	8369,8610,	MTTC01000001.g3	unk	unk	0,2,
585	MTTC01000001.g4.t1	MTTC01000001	+	8674	9367	8674	9367	1	8674,	9367,	MTTC01000001.g4	unk	unk	0,
585	MTTC01000001.g5.t1	MTTC01000001	+	9444	21330	9444	21330	9	9444,10973,11672,12356,12532,14384,15089,16144,20840,	9577,11492,11857,12485,12704,14786,15224,16259,21330,	MTTC01000001.g5	unk	unk	0,1,1,0,0,1,1,1,2,
585	MTTC01000002.g6.t1	MTTC01000002	+	0	227	0	227	1	0,	227,	MTTC01000002.g6	unk	unk	1,
585	MTTC01000002.g7.t1	MTTC01000002	+	256	1224	256	1224	2	256,1040,	993,1224,	MTTC01000002.g7	unk	unk	0,2,
585	MTTC01000002.g8.t1	MTTC01000002	+	1360	2394	1360	2394	3	1360,1877,2204,	1815,2120,2394,	MTTC01000002.g8	unk	unk	0,2,2,
585	MTTC01000002.g9.t1	MTTC01000002	-	2613	3540	2613	3540	1	2613,	3540,	MTTC01000002.g9	unk	unk	0,
585	MTTC01000002.g10.t1	MTTC01000002	+	3603	4317	3603	4317	2	3603,3763,	3688,4317,	MTTC01000002.g10	unk	unk	0,1,

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