Question about augustus/blat

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Question about augustus/blat

Shane Brubaker-2
Hi, can you tell me how Maker uses the cDNA evidence with Augustus, without using Blat?  Does it use exonerate?

I am asking because I want to use cDNA hints with Augustus in some of my own code, but I don't have Blat.  I am wondering how maker does it.  Also, is the intermediate hints file stored somewhere by maker?

Thanks.

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Re: Question about augustus/blat

Carson Hinton Holt
Re: [maker-devel] Question about augustus/blat Yes.  MAKER uses exonerate.  First MAKER runs BLAST, then it filters those and runs exonerate using the BLAST coordinates.  This is much faster than just running exonerate on the entire genome.

The xdef files used to send hints are stored in theVoid directory for each contig.  If they are not there, you can force them to be there by commenting out a line in the maker/lib/Widget/augustus.pm file.
The line is --> unlink($xdef_file) if(-f $xdef_file);

Thanks,
Carson

On 6/28/11 12:27 PM, "Shane Brubaker" <sbrubaker@...> wrote:

Hi, can you tell me how Maker uses the cDNA evidence with Augustus, without using Blat?  Does it use exonerate?

I am asking because I want to use cDNA hints with Augustus in some of my own code, but I don't have Blat.  I am wondering how maker does it.  Also, is the intermediate hints file stored somewhere by maker?

Thanks.

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Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah

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