Schema for genBlastG Genes - genBlastG Gene Predictions

Database: DkikGB2 Primary Table: genblastg Row Count: 30,173 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	gbg_CG4783-PB_0	`varchar(255)`	values
`chrom`	AFFH02000335	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	35160	`int(10) unsigned`	range
`txEnd`	35457	`int(10) unsigned`	range
`cdsStart`	35160	`int(10) unsigned`	range
`cdsEnd`	35457	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	35160,35398,	`longblob`
`exonEnds`	35341,35457,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	gbg_CG4783-PB_0	AFFH02000335	-	35160	35457	35160	35457	2	35160,35398,	35341,35457,
585	gbg_CG4783-PA_1	AFFH02000335	-	35160	35457	35160	35457	2	35160,35398,	35341,35457,
585	gbg_CG46042-PC_2	AFFH02000335	+	41773	42135	41773	42135	2	41773,41894,	41825,42135,
585	gbg_Hs6st-PA_3	AFFH02000335	+	48691	58251	48691	58251	5	48691,48841,49060,49668,58115,	48808,48997,49609,49853,58251,
585	gbg_Hs6st-PB_4	AFFH02000335	+	48691	58251	48691	58251	5	48691,48841,49060,49668,58115,	48808,48997,49609,49853,58251,
585	gbg_mira-PA_5	AFFH02000335	+	53149	55654	53149	55654	1	53149,	55654,
585	gbg_mira-PC_6	AFFH02000335	+	53149	55654	53149	55654	2	53149,55006,	54934,55654,
585	gbg_mira-PB_7	AFFH02000335	+	53149	55654	53149	55654	2	53149,55024,	54934,55654,
585	gbg_CG4459-PA_8	AFFH02000335	+	59961	62179	59961	62179	5	59961,60094,60700,60943,61628,	59963,60640,60855,61570,62179,
585	gbg_CG4462-PA_9	AFFH02000335	+	64891	67887	64891	67887	4	64891,65637,67284,67489,	65570,66144,67428,67887,

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. kikkawai (DkikGB2) assembly and the predicted gene models were constructed using genBlastG. Methods D. melanogaster protein sequences were aligned against the D. kikkawai (DkikGB2) 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