Schema for genBlastG Genes - genBlastG Gene Predictions

Database: DpseGB3 Primary Table: genblastg Row Count: 29,689 Data last updated: 2024-08-24

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	gbg_CG13991-PA_0	`varchar(255)`	values
`chrom`	CH379058	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	17120	`int(10) unsigned`	range
`txEnd`	54416	`int(10) unsigned`	range
`cdsStart`	17120	`int(10) unsigned`	range
`cdsEnd`	54416	`int(10) unsigned`	range
`exonCount`	6	`int(10) unsigned`	range
`exonStarts`	17120,20189,22145,53659,542...	`longblob`
`exonEnds`	19955,22115,22491,53685,543...	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	gbg_CG13991-PA_0	CH379058	-	17120	54416	17120	54416	6	17120,20189,22145,53659,54284,54406,	19955,22115,22491,53685,54364,54416,
585	gbg_WDR79-PC_1	CH379058	+	54780	70371	54780	70371	6	54780,55510,68601,68901,69164,69530,	54785,55617,68772,69047,69475,70371,
585	gbg_CG9222-PA_2	CH379058	+	57285	58473	57285	58473	5	57285,57379,57841,58214,58329,	57325,57776,58152,58279,58473,
585	gbg_B9d2-PA_3	CH379058	+	58811	59477	58811	59477	3	58811,58972,59383,	58899,59324,59477,
585	gbg_tctn-PA_4	CH379058	+	59479	61516	59479	61516	1	59479,	61516,
73	gbg_CG31642-PA_5	CH379058	-	60692	160274	60692	160274	4	60692,64720,80134,160261,	60952,64794,81737,160274,
585	gbg_sac-PB_6	CH379058	-	61562	65074	61562	65074	2	61562,65022,	64744,65074,
585	gbg_WDR79-PB_7	CH379058	+	68417	70371	68417	70371	5	68417,68601,68901,69164,69530,	68424,68772,69047,69475,70371,
585	gbg_Arpc4-PA_8	CH379058	-	70546	71053	70546	71053	1	70546,	71053,
585	gbg_stai-PD_9	CH379058	-	74330	113866	74330	113866	8	74330,74559,75375,75584,75859,78205,113087,113860,	74417,74715,75522,75770,76029,78551,113162,113866,

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. pseudoobscura (DpseGB3) assembly and the predicted gene models were constructed using genBlastG. Methods D. melanogaster protein sequences were aligned against the D. pseudoobscura (DpseGB3) 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