Schema for genBlastG Genes - genBlastG Gene Predictions

Database: DsimGB2 Primary Table: genblastg Row Count: 30,804 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	gbg_l(2)gl-PF_0	`varchar(255)`	values
`chrom`	CM002910	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	5294	`int(10) unsigned`	range
`txEnd`	9710	`int(10) unsigned`	range
`cdsStart`	5294	`int(10) unsigned`	range
`cdsEnd`	9710	`int(10) unsigned`	range
`exonCount`	7	`int(10) unsigned`	range
`exonStarts`	5294,5487,5858,6373,7581,77...	`longblob`
`exonEnds`	5424,5596,6301,7016,7687,89...	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	gbg_l(2)gl-PF_0	CM002910	-	5294	9710	5294	9710	7	5294,5487,5858,6373,7581,7744,8994,	5424,5596,6301,7016,7687,8936,9710,
585	gbg_l(2)gl-PE_1	CM002910	-	5294	9710	5294	9710	7	5294,5487,5858,6373,7581,7744,8994,	5424,5596,6301,7016,7687,8936,9710,
585	gbg_l(2)gl-PD_2	CM002910	-	5294	9710	5294	9710	7	5294,5487,5858,6373,7581,7744,8994,	5424,5596,6301,7016,7687,8936,9710,
585	gbg_l(2)gl-PC_3	CM002910	-	5294	11255	5294	11255	8	5294,5487,5858,6373,7581,7744,8994,11171,	5424,5596,6301,7016,7687,8936,9773,11255,
585	gbg_l(2)gl-PB_4	CM002910	-	5294	11255	5294	11255	8	5294,5487,5858,6373,7581,7744,8994,11183,	5424,5596,6301,7016,7687,8936,9773,11255,
585	gbg_l(2)gl-PG_5	CM002910	-	5294	11255	5294	11255	8	5294,5487,5858,6373,7581,7744,8994,11171,	5424,5596,6301,7016,7687,8936,9773,11255,
585	gbg_l(2)gl-PA_6	CM002910	-	5294	11255	5294	11255	8	5294,5487,5858,6373,7581,7744,8994,11171,	5424,5596,6301,7016,7687,8936,9773,11255,
585	gbg_l(2)gl-PI_7	CM002910	-	5294	11255	5294	11255	8	5294,5487,5858,6373,7581,7744,8994,11171,	5424,5596,6301,7016,7687,8936,9773,11255,
585	gbg_l(2)gl-PH_8	CM002910	-	5294	11255	5294	11255	8	5294,5487,5858,6373,7581,7744,8994,11171,	5424,5596,6301,7016,7687,8936,9773,11255,
585	gbg_l(2)gl-PJ_9	CM002910	-	5294	11255	5294	11255	8	5294,5487,5858,6373,7581,7744,8994,11171,	5424,5596,6301,7016,7687,8936,9773,11255,

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. simulans (DsimGB2) assembly and the predicted gene models were constructed using genBlastG. Methods D. melanogaster protein sequences were aligned against the D. simulans (DsimGB2) 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