Schema for genBlastG Genes - genBlastG Gene Predictions

Database: DbiaGB2 Primary Table: genblastg Row Count: 30,479 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	gbg_Pcmt-PC_0	`varchar(255)`	values
`chrom`	AFFD02000037	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	2935	`int(10) unsigned`	range
`txEnd`	3861	`int(10) unsigned`	range
`cdsStart`	2935	`int(10) unsigned`	range
`cdsEnd`	3861	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	2935,3051,3441,	`longblob`
`exonEnds`	2990,3188,3861,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	gbg_Pcmt-PC_0	AFFD02000037	+	2935	3861	2935	3861	3	2935,3051,3441,	2990,3188,3861,
585	gbg_Pcmt-PA_1	AFFD02000037	+	2935	3990	2935	3990	4	2935,3051,3441,3906,	2990,3188,3846,3990,
585	gbg_mia-PA_2	AFFD02000037	+	5263	7468	5263	7468	4	5263,6079,6639,7090,	6022,6258,7042,7468,
585	gbg_mia-PB_3	AFFD02000037	+	5263	7468	5263	7468	4	5263,6079,6639,7090,	6022,6258,7042,7468,
585	gbg_mia-PC_4	AFFD02000037	+	5263	7468	5263	7468	4	5263,6079,6639,7090,	6022,6258,7042,7468,
585	gbg_CG2519-PC_5	AFFD02000037	+	9170	15215	9170	15215	11	9170,9460,10784,11264,12565,12981,13492,13650,14015,14363,15008,	9402,9668,11106,12474,12925,13439,13591,13961,14298,14528,15215,
585	gbg_CG2519-PB_6	AFFD02000037	+	9170	15215	9170	15215	11	9170,9460,10784,11264,12565,12981,13492,13650,14015,14363,15008,	9402,9668,11106,12474,12925,13439,13591,13961,14298,14528,15215,
585	gbg_CG2519-PA_7	AFFD02000037	+	9170	15215	9170	15215	12	9170,9460,10122,10784,11264,12565,12981,13492,13650,14015,14363,15008,	9402,9668,10194,11106,12474,12925,13439,13591,13961,14298,14528,15215,
585	gbg_Ucp4C-PA_8	AFFD02000073	+	23544	24552	23544	24552	1	23544,	24552,
585	gbg_Alg-2-PC_9	AFFD02000187	+	8643	9246	8643	9246	3	8643,8755,9208,	8702,9147,9246,

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. biarmipes (DbiaGB2) assembly and the predicted gene models were constructed using genBlastG. Methods D. melanogaster protein sequences were aligned against the D. biarmipes (DbiaGB2) 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