Schema for genBlastG Genes - genBlastG Gene Predictions

Database: DmirGB2 Primary Table: genblastg Row Count: 29,490 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	gbg_Cyp311a1-PB_0	`varchar(255)`	values
`chrom`	CM001516	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	15164	`int(10) unsigned`	range
`txEnd`	16790	`int(10) unsigned`	range
`cdsStart`	15164	`int(10) unsigned`	range
`cdsEnd`	16790	`int(10) unsigned`	range
`exonCount`	7	`int(10) unsigned`	range
`exonStarts`	15164,15381,15810,15964,160...	`longblob`
`exonEnds`	15315,15759,15923,16012,161...	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	gbg_Cyp311a1-PB_0	CM001516	+	15164	16790	15164	16790	7	15164,15381,15810,15964,16050,16218,16382,	15315,15759,15923,16012,16158,16281,16790,
585	gbg_CG14106-PA_1	CM001516	+	16624	18026	16624	18026	7	16624,17000,17087,17188,17368,17534,17777,	16645,17048,17152,17326,17471,17732,18026,
585	gbg_CG4281-PA_2	CM001516	+	18571	21141	18571	21141	11	18571,18747,18878,19012,19130,19314,19436,19737,20432,20817,21100,	18689,18846,18973,19050,19284,19406,19687,20372,20737,20936,21141,
585	gbg_Sik2-PA_3	CM001516	+	22823	29360	22823	29360	13	22823,23633,24179,24309,24698,25337,26090,26350,26518,26751,27531,27865,29252,	22886,24113,24243,24596,25169,25926,26296,26439,26688,27480,27811,28247,29360,
585	gbg_CG4313-PC_4	CM001516	-	30530	31729	30530	31729	3	30530,31094,31488,	30999,31437,31729,
585	gbg_CG4313-PE_5	CM001516	-	30530	31729	30530	31729	3	30530,31094,31488,	30999,31437,31729,
585	gbg_CG4313-PD_6	CM001516	-	30530	95652	30530	95652	6	30530,31094,31488,31826,52255,95578,	30999,31437,31757,32176,52424,95652,
585	gbg_moody-PC_7	CM001516	+	41785	44241	41785	44241	6	41785,42274,42504,43079,43579,43891,	41862,42415,43049,43505,43729,44241,
585	gbg_moody-PD_8	CM001516	+	41785	44241	41785	44241	6	41785,42274,42504,43079,43579,43891,	41862,42415,43049,43505,43729,44241,
585	gbg_moody-PF_9	CM001516	+	41785	44350	41785	44350	5	41785,42274,42504,43079,43577,	41862,42415,43049,43505,44350,

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. miranda (DmirGB2) assembly and the predicted gene models were constructed using genBlastG. Methods D. melanogaster protein sequences were aligned against the D. miranda (DmirGB2) 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