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genBlastG Gene Predictions   (All Genes and Gene Prediction Tracks)

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Data last updated at UCSC: 2024-08-24

Description

D. melanogaster proteins from FlyBase were aligned against each scaffold in the D. simulans (DsimGB2) assembly and the predicted gene models were constructed using genBlastG.

Methods

D. melanogaster protein sequences were aligned against the D. simulans (DsimGB2) 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.