Schema for genBlastG Genes - genBlastG Gene Predictions

Database: DtakGB2 Primary Table: genblastg Row Count: 30,605 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	gbg_d4-PD_2	`varchar(255)`	values
`chrom`	AFFI02000003	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	10545	`int(10) unsigned`	range
`txEnd`	32417	`int(10) unsigned`	range
`cdsStart`	10545	`int(10) unsigned`	range
`cdsEnd`	32417	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	10545,30915,31969,	`longblob`
`exonEnds`	11330,31179,32417,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	gbg_d4-PD_2	AFFI02000003	-	10545	32417	10545	32417	3	10545,30915,31969,	11330,31179,32417,
585	gbg_d4-PB_0	AFFI02000003	-	10545	31153	10545	31153	2	10545,30912,	11330,31153,
585	gbg_d4-PC_3	AFFI02000003	-	10545	32417	10545	32417	3	10545,30918,31969,	11330,31179,32417,
585	gbg_d4-PA_1	AFFI02000003	-	10545	32417	10545	32417	3	10545,30912,31969,	11330,31179,32417,
585	gbg_CG3107-PA_4	AFFI02000003	+	10949	42477	10949	42477	4	10949,11041,39383,39950,	10969,11050,39896,42477,
585	gbg_CG3107-PB_5	AFFI02000003	+	10949	42477	10949	42477	4	10949,11041,39383,39950,	10969,11050,39896,42477,
585	gbg_CG3107-PD_6	AFFI02000003	+	10949	42477	10949	42477	4	10949,11041,39383,39950,	10969,11050,39896,42477,
585	gbg_CG3107-PC_7	AFFI02000003	+	10949	42477	10949	42477	4	10949,11041,39383,39950,	10969,11050,39896,42477,
585	gbg_yellow-e-PA_8	AFFI02000009	+	10234	12297	10234	12297	2	10234,11516,	11046,12297,
585	gbg_yellow-e2-PB_9	AFFI02000009	+	15390	17120	15390	17120	3	15390,15454,16065,	15392,15708,17120,

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

genBlastG Genes (genblastg) Track Description


	Description D. melanogaster proteins from FlyBase were aligned against each scaffold in the D. takahashii (DtakGB2) assembly and the predicted gene models were constructed using genBlastG. Methods D. melanogaster protein sequences were aligned against the D. takahashii (DtakGB2) genome assembly using WU-TBLASTN with the following parameters: -B=1000 -V=1000 -hspmax=5000 -hspsepSmax=50000 -hspsepQmax=1000 -altscore='any * -999' -nogaps -hitdist=40 -matrix=BLOSUM80 -Q=12 -R=2 -e 1e-10 -wordmask=seg+xnu -topComboN=1 -links -notes -warnings -novalidctxok The WU-TBLASTN results were then analyzed by genBlastG using the following parameters: `-P wublast -r 1 -i 30 -pro -gff -e 1e-10` References She R, Chu JS, Uyar B, Wang J, Wang K, Chen N. genBlastG: using BLAST searches to build homologous gene models. Bioinformatics. 2011 Aug 1;27(15):2141-3.

Description