[Bioperl-l] Remote BLAST and BLAST Word Size

[Jason Stajich]

I think you can do it with:
(make sure you use a sensible size depending on if you are using BLASTN or
BLASTP)

$Bio::Tools::Run::RemoteBlast::HEADER{'WORD_SIZE'} =12;

But as always - if you want it to be faster, consider running BLAST
locally on your own system. You position in the NCBI queue is inversely
proportional  to the number of jobs you have submitted...


On Sat, 15 Feb 2003, Henrik Nilsson wrote:

> Hello
>
> I am under the understanding that increasing the BLAST Word length may
> increase BLAST speed, and I'd like to play around with it so see what I
> can get. Is it possible to set the word length in bioperl's remote
> BLAST, something like
>
> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} =   'mouse[ORGN]
> AND 17[WS]';
>
> ? Or are there any other non-GUI ways of achieving this?
>
> Thanks,
>
> Henrik N
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu