[Bioperl-l] Proposed bioperl module for local running of the NCBI standalone blastpackage

[chris dagdigian]

Count me in as someone who is interested in a Bioperl 'Disperse'
wrapper.

-Chris


Chris Dagdigian         (Home:Work) Blackstone Technology Group
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On Mon, 16 Oct 2000, Aaron J Mackey wrote:

> 
> On Mon, 16 Oct 2000, Hilmar Lapp wrote:
> 
> > Basically, I have one comment. It would be very helpful if such a module
> > could also support running stand-alone BLASTs in parallel, e.g., if
> > you've got a multi-processor machine. I know that the current NCBI BLAST
> > supports multi-threading, but on well-equipped machines it often scales
> > better to run multiple processes.
> 
> If there's enough interest, I would consider writing a bioperl wrapper for
> 'disperse' (which accomplishes batch parallelization via multiple
> processes on potentially many different machines).  See:
> 
> Raphael Clifford and Aaron J. Mackey 
> Disperse: a simple and efficient approach to parallel database searching 
> Bioinformatics 2000 16: 564-565.
> 
> http://www.bioinformatics.oupjournals.org/cgi/content/abstract/16/6/564
> 
> But even as it stands, if you wanted to obtain a stream of blast hits, you
> could replace your system call to blast with a system call to disperse
> (printing your query library to disperse's STDIN and reading it's STDOUT
> via Open3 or somesuch).
> 
> -Aaron
> 
> -- 
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> / Aaron J Mackey           \
> \  Dr. Pearson Laboratory  / 
>  \ University of Virginia  \     
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