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

Aaron J Mackey ajm6q@virginia.edu
Mon, 16 Oct 2000 09:38:02 -0400 (EDT)

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.


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).


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