Schema for genBlastG Genes - genBlastG Gene Predictions

Database: DobsGB1 Primary Table: genblastg Row Count: 30,207 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	gbg_CG6066-PA_0	`varchar(255)`	values
`chrom`	BDQP01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	11736	`int(10) unsigned`	range
`txEnd`	87784	`int(10) unsigned`	range
`cdsStart`	11736	`int(10) unsigned`	range
`cdsEnd`	87784	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	11736,86467,86906,	`longblob`
`exonEnds`	11814,86876,87784,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	gbg_CG6066-PA_0	BDQP01000001	+	11736	87784	11736	87784	3	11736,86467,86906,	11814,86876,87784,
585	gbg_Ser-PA_1	BDQP01000001	+	14012	32204	14012	32204	16	14012,14167,18205,18970,23291,23671,25913,26185,26487,27912,28843,28903,29149,30315,30773,31448,	14059,14324,18323,19158,23346,23987,26047,26361,26722,28683,28864,29077,29245,30687,31387,32204,
585	gbg_Ser-PB_2	BDQP01000001	+	14012	32204	14012	32204	16	14012,14167,18205,18970,23291,23671,25913,26185,26487,27912,28843,28903,29149,30315,30773,31448,	14059,14324,18323,19158,23346,23987,26047,26361,26722,28683,28864,29077,29245,30687,31387,32204,
585	gbg_spn-D-PA_3	BDQP01000001	-	37921	86979	37921	86979	7	37921,38186,38378,38594,38769,86461,86967,	38092,38315,38536,38701,38895,86607,86979,
585	gbg_CG34293-PB_4	BDQP01000001	+	39339	39661	39339	39661	2	39339,39503,	39436,39661,
585	gbg_CG34293-PA_5	BDQP01000001	+	39339	39661	39339	39661	2	39339,39503,	39436,39661,
585	gbg_ppk31-PB_6	BDQP01000001	-	39758	41806	39758	41806	6	39758,39984,40149,40864,41134,41773,	39925,40091,40805,41081,41220,41806,
585	gbg_CG1773-PA_7	BDQP01000001	-	42650	96798	42650	96798	10	42650,42832,43107,46378,46501,46772,68775,79253,96619,96766,	42696,43023,43152,46428,46695,46821,68823,79335,96716,96798,
585	gbg_CG5909-PA_8	BDQP01000001	-	42804	124739	42804	124739	5	42804,43483,43884,80934,124694,	43414,43812,44035,80954,124739,
585	gbg_grass-PA_9	BDQP01000001	-	46003	47303	46003	47303	5	46003,46501,46772,46886,47177,	46428,46695,46821,47100,47303,

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. obscura (DobsGB1) assembly and the predicted gene models were constructed using genBlastG. Methods D. melanogaster protein sequences were aligned against the D. obscura (DobsGB1) 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