Schema for genBlastG Genes - genBlastG Gene Predictions |
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Database: DgriCAF1 Primary Table: genblastg Row Count: 30,529 Data last updated: 2024-01-05
| field | example | SQL type | info |
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| bin | 585 | smallint(5) unsigned | range |
| name | gbg_SMC5-PF_1 | varchar(255) | values |
| chrom | scaffold_10030 | varchar(255) | values |
| strand | + | char(1) | values |
| txStart | 5624 | int(10) unsigned | range |
| txEnd | 22528 | int(10) unsigned | range |
| cdsStart | 5624 | int(10) unsigned | range |
| cdsEnd | 22528 | int(10) unsigned | range |
| exonCount | 16 | int(10) unsigned | range |
| exonStarts | 5624,6750,7208,8379,8851,92... | longblob | |
| exonEnds | 5698,7123,7387,8626,9139,93... | longblob | |
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Sample Rows
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| bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds |
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| 585 | gbg_SMC5-PF_1 | scaffold_10030 | + | 5624 | 22528 | 5624 | 22528 | 16 | 5624,6750,7208,8379,8851,9210,15139,15394,15754,16569,16833,17146,17394,21755,22255,22432, | 5698,7123,7387,8626,9139,9312,15328,15569,15881,16775,17051,17332,17619,21913,22373,22528, |
| 585 | gbg_SMC5-PH_3 | scaffold_10030 | + | 5624 | 22528 | 5624 | 22528 | 16 | 5624,6750,7208,8379,8851,9210,15139,15394,15754,16569,16833,17146,17394,21755,22255,22432, | 5698,7123,7387,8626,9139,9312,15328,15569,15881,16775,17051,17332,17616,21913,22373,22528, |
| 585 | gbg_SMC5-PG_2 | scaffold_10030 | + | 5624 | 22528 | 5624 | 22528 | 16 | 5624,6750,7208,8379,8795,9210,15139,15394,15754,16569,16833,17146,17394,21755,22255,22432, | 5698,7123,7387,8630,9139,9312,15328,15569,15881,16775,17051,17332,17616,21913,22373,22528, |
| 585 | gbg_SMC5-PE_0 | scaffold_10030 | + | 5624 | 22528 | 5624 | 22528 | 16 | 5624,6750,7208,8379,8795,9210,15139,15394,15754,16569,16833,17146,17394,21755,22255,22432, | 5698,7123,7387,8630,9139,9312,15328,15569,15881,16775,17051,17332,17619,21913,22373,22528, |
| 585 | gbg_CG30270-PD_4 | scaffold_10033 | + | 632 | 884 | 632 | 884 | 1 | 632, | 884, |
| 585 | gbg_CG31816-PA_5 | scaffold_10066 | + | 206 | 679 | 206 | 679 | 3 | 206,335,502, | 219,442,679, |
| 585 | gbg_His3:CG33821-PA_6 | scaffold_10273 | - | 145 | 556 | 145 | 556 | 1 | 145, | 556, |
| 585 | gbg_His3:CG33815-PA_7 | scaffold_10273 | - | 145 | 556 | 145 | 556 | 1 | 145, | 556, |
| 585 | gbg_His3:CG33860-PA_8 | scaffold_10273 | - | 145 | 556 | 145 | 556 | 1 | 145, | 556, |
| 585 | gbg_His3:CG33836-PA_9 | scaffold_10273 | - | 145 | 556 | 145 | 556 | 1 | 145, | 556, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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genBlastG Genes (genblastg) Track Description
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Description
D. melanogaster proteins from FlyBase were aligned against each
scaffold in the D. grimshawi (DgriCAF1) assembly and the predicted gene models were constructed
using genBlastG.
Methods
D. melanogaster protein sequences were aligned against the D. grimshawi (DgriCAF1) 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.
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