[Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Thu Nov 16 19:19:42 EST 2006


Andrew,

>> Anyone have any opinions as to how easy/difficult it would be 
>> to incorporate mpiblast into 
>> Bio::Tools::Run::StandAloneBlast?  It runs essentially the 
>> same way as blastall, and its output is nearly identical.

> I think plans were to rewrite StandAloneBlast and RemoteBlast to make them
> more 'generic' (i.e. capable of running other BLAST-related programs),
> though I'm not sure at what stage everything is.  

Chris is correct is saying there were plans to rewrite the Blast modules 
- at the time myself, Roger Hall, Chris? and Jason were involved, but 
unfortunately Roger fell ill in Feb 2006 and had to have urgent heart 
surgery. (And my wife had a baby :-)

Here's some of the early discussion:
http://portal.open-bio.org/pipermail/bioperl-l/2006-February/020745.html

ANYWAY, I think it might be possible to incorporate mpiblast easily, 
even without changing Bioperl if we are lucky, via the ->executable() 
setter method. If not, I added rpsblast support last year which is 
similar to blastall, so it'd probably be achievable.

How does the the output of mpiblast differ to NCBI blastall ?
What command line options does mpiblast take?

-- 
Dr Torsten Seemann               http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia



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