[Bioperl-l] Regarding blast in Bioperl

Bernd Web bernd.web at gmail.com
Thu Jan 21 13:37:18 EST 2010


Regarding RemoteBlast, my I add a query?
It seems that Bio::Tools::Run::RemoteBlast  is sending each sequence
seperately to the NCBI (at least in BP 1.5.2).
This means that for each Sequence a RID is to be checked. Is this
indeed the case?
The BLAST URL-API or batch interface supports sending multiple
sequences at once.


On Thu, Jan 21, 2010 at 7:28 PM, Roopa Raghuveer <rtbio.2009 at gmail.com> wrote:
> Hello Mark,
> This is Roopa again. I have a small problem again. I am working on Remote
> blast. The program works well. But the problem is this.  The program
> accesses the server and gets the output correctly. I am trying to send the
> result sequences into an array and I found that always the first sequence
> among the Result sequences is missing. The code is
>  my $str = Bio::SeqIO->new('-file' => $nuc , '-format' => 'fasta' ,
> '-organism' => "$organ\[ORGN]");

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