[Bioperl-l] ACC -> Organism question

[Wiepert, Mathieu]

Hi,

If you already have a sequence object loaded, something similar to this works I think...

    my $species;
    eval { $species = $seq->species()};
    if (defined $species) {
      if ($species->ncbi_taxid() == 9606) {
        $out->write_seq($seq);
      }
    }

look at the Bio::Seq object for the species method, and then the species object http://docs.bioperl.org/bioperl-live/Bio/Species.html to see what else you can see from it. 

Do you have the seq loaded already?  Or just the accnum.  I load the seq from a genbank file, a fast file might not have all the features, not sure what you are working from.

-Mat

-----Original Message-----
From: Henrik Nilsson [mailto:henrik.nilsson at botany.gu.se]
Sent: Tuesday, February 18, 2003 10:29 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] ACC -> Organism question


Hi,

If I have a valid Genbank accession number, is there some automated way
to find out to what organism the sequence belongs? I'd like send a valid
Genbank accession number and get back the organism name - can this be
done using bioperl?

If not, how would you do it?

Yours,

Henrik Nilsson



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