[Bioperl-l] bio::tools::run::blat?

[Jason Stajich]

Bio::Tools::Run::Alignment::Blat
In the bioperl-run CVS repository and in the bioperl-run distro.

Any new "standalone-xxx" should be written in the bioperl runnable way.
StandAloneBlast is legacy code in many ways and pretty hard to manage.

Will Spooner at Ensembl has written some very nice generic pairwise
alignment search interfaces that allow dispatching of Fasta,SSAHA, Blast,
etc.  One day we may be able to import some more of his nice design into
the system.

-jason

On Wed, 10 Mar 2004, Sean Davis wrote:

> Just a quick question:  Has anyone considered (or achieved) the blat
> equivalent of standaloneblast?
>
> Thanks,
> Sean
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu