Description
D. melanogaster proteins from FlyBase were aligned against each
scaffold in the D. yakuba (DyakCAF1) assembly and the predicted gene models were constructed
using genBlastG.
Methods
D. melanogaster protein sequences were aligned against the D. yakuba (DyakCAF1) 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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