[Bioperl-l] producing an organism report from BLAST results?

[Marc Logghe]

Hi Tim,
I am getting confused. Are you looking for a way to get your hands on the taxblast report as a result of performing a remote blast @ NCBI. Or rather, trying to implement locally a blast facility producing a taxblast report similar to the NCBI web site ?
Regards,
Marc

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org on behalf of Tim Reid
Sent: Tue 11/22/2005 9:38 PM
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] producing an organism report from BLAST results?
 
On 11/22/05, Barry Moore <bmoore at genetics.utah.edu> wrote:
>
>  $Bio::Tools::Run::RemoteBlast::HEADER{'NCBI_GI'} = 'yes';
>
> The above example should be equivalent to the blastall -I T option.
>
by looking thru the source (which appears to be rather out of sync with the
documentation) i discovered that this line has to be:

$Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'NCBI_GI'} = 'yes';

because NCBI_GI is a paramater of the GET cmd.

this is an odd arrangement (shouldn't these paramaters be set via the
RemoteBlast constructor?) but it works.

i have not yet been able to obtain the taxonomy relating to a gi number, but
i am still working at it.

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