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

Database: DobsGB1 Primary Table: augustusBUSCO Row Count: 16,945 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	BDQP01000001.g1.t1	`varchar(255)`	values
`chrom`	BDQP01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	2102	`int(10) unsigned`	range
`txEnd`	2438	`int(10) unsigned`	range
`cdsStart`	2102	`int(10) unsigned`	range
`cdsEnd`	2438	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	2102,	`longblob`
`exonEnds`	2438,	`longblob`
`score`	0	`int(11)`	range
`name2`	BDQP01000001.g1	`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	BDQP01000001.g1.t1	BDQP01000001	+	2102	2438	2102	2438	1	2102,	2438,	BDQP01000001.g1	unk	unk	0,
585	BDQP01000001.g2.t1	BDQP01000001	-	5849	6254	5849	6254	1	5849,	6254,	BDQP01000001.g2	unk	unk	0,
585	BDQP01000001.g3.t1	BDQP01000001	+	17424	32204	17424	32204	14	17424,18205,18970,23291,23671,25913,26185,26487,27912,28843,29149,30315,30773,31448,	17433,18323,19158,23346,23987,26047,26361,26722,28683,29077,29245,30687,31387,32204,	BDQP01000001.g3	unk	unk	0,0,1,0,1,2,1,0,1,1,1,1,1,0,
585	BDQP01000001.g4.t1	BDQP01000001	-	37921	41286	37921	41286	10	37921,38168,38378,38594,39369,39863,39984,40149,40864,41134,	38092,38315,38536,38694,39408,39925,40091,40805,41081,41286,	BDQP01000001.g4	unk	unk	0,0,1,0,0,1,2,0,2,0,
585	BDQP01000001.g5.t1	BDQP01000001	-	42804	54552	42804	54552	15	42804,43483,43884,44134,46007,46501,46772,46886,47177,49733,49970,50335,50566,51679,54535,	43414,43812,44039,44232,46428,46695,46821,47100,47350,49898,50265,50488,51616,51869,54552,	BDQP01000001.g5	unk	unk	2,0,1,2,1,2,1,0,1,1,0,0,0,2,0,
585	BDQP01000001.g6.t1	BDQP01000001	+	69248	76079	69248	76079	6	69248,73000,73214,74288,74855,75061,	69260,73141,73969,74594,74987,76079,	BDQP01000001.g6	unk	unk	0,0,0,2,2,2,
585	BDQP01000001.g7.t1	BDQP01000001	+	78088	80958	78088	80958	4	78088,78665,79350,79729,	78594,79283,79667,80958,	BDQP01000001.g7	unk	unk	0,2,2,1,
585	BDQP01000001.g8.t1	BDQP01000001	-	81011	83963	81011	83963	7	81011,81340,82353,82732,83244,83591,83870,	81287,82302,82670,83181,83534,83811,83963,	BDQP01000001.g8	unk	unk	0,1,2,0,1,0,0,
585	BDQP01000001.g9.t1	BDQP01000001	-	84301	85756	84301	85756	6	84301,84469,84855,85127,85499,85712,	84407,84795,85067,85437,85647,85756,	BDQP01000001.g9	unk	unk	2,0,1,0,2,0,
585	BDQP01000001.g10.t1	BDQP01000001	+	86299	87784	86299	87784	1	86299,	87784,	BDQP01000001.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

Methods

References