[Bioperl-l] remoteblast doesn't save the Output File

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Mon Dec 5 22:05:53 EST 2005

On Mon, 2005-12-05 at 18:32 -0600, Hubert Prielinger wrote:
> Hello Torsten,
> thanks for your Response, I have already managed to run the program, 
> thank you very much.
> but I still have the Problem, that I don't know how set the Gap 
> Parameters, because I want to use PAM30, but
> it doesn't work with the Default Parameters......
> If you know how to change them, I would really appreciate telling me. I 
> have tried "gap" and "ext", but it doesn't work.
> and I can't find anything online...

If you read the module manual page 
ie. perldoc Bio::Tools::Run::RemoteBlast
there is an example - just set:

$Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = 'PAM30';

'MATRIX_NAME' is just one possibility, the perldoc
refers to this http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html
which has the 'GAP_COSTS' you are looking for:

Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
Victorian Bioinformatics Consortium

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