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

Database: DpseGB3 Primary Table: augustusBUSCO Row Count: 13,892 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CH379058.g1.t1	`varchar(255)`	values
`chrom`	CH379058	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	0	`int(10) unsigned`	range
`txEnd`	557	`int(10) unsigned`	range
`cdsStart`	0	`int(10) unsigned`	range
`cdsEnd`	557	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	0,279,541,	`longblob`
`exonEnds`	217,477,557,	`longblob`
`score`	0	`int(11)`	range
`name2`	CH379058.g1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	CH379058.g1.t1	CH379058	-	0	557	0	557	3	0,279,541,	217,477,557,	CH379058.g1	unk	unk	1,1,0,
585	CH379058.g2.t1	CH379058	-	17120	22628	17120	22628	1	17120,	22628,	CH379058.g2	unk	unk	0,
585	CH379058.g3.t1	CH379058	+	49114	49327	49114	49327	1	49114,	49327,	CH379058.g3	unk	unk	0,
585	CH379058.g4.t1	CH379058	+	57285	59364	57285	59364	6	57285,57379,57841,58214,58341,59097,	57325,57776,58152,58279,58464,59364,	CH379058.g4	unk	unk	0,1,2,1,0,0,
585	CH379058.g5.t1	CH379058	+	59479	61516	59479	61516	1	59479,	61516,	CH379058.g5	unk	unk	0,
585	CH379058.g6.t1	CH379058	-	61562	64766	61562	64766	1	61562,	64766,	CH379058.g6	unk	unk	0,
585	CH379058.g7.t1	CH379058	+	68485	70371	68485	70371	3	68485,68601,69530,	68537,69475,70371,	CH379058.g7	unk	unk	0,1,2,
585	CH379058.g8.t1	CH379058	-	70546	71053	70546	71053	1	70546,	71053,	CH379058.g8	unk	unk	0,
585	CH379058.g9.t1	CH379058	-	74330	78590	74330	78590	6	74330,74559,75375,75584,75859,78100,	74417,74715,75522,75770,76029,78590,	CH379058.g9	unk	unk	0,0,0,0,1,0,
585	CH379058.g10.t1	CH379058	-	79461	81852	79461	81852	1	79461,	81852,	CH379058.g10	unk	unk	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