Bioperl: Extracting genes from GenBank flat file

[Luca.Toldo@merck.de]

dear Gert,
I suggest you using Boulder::Genbank module.
That does it for you already.
regards
luca




gert.thijs@esat.kuleuven.ac.be on 06.06.2000 13:39:39

To:   vsns-bcd-perl@lists.uni-bielefeld.de
cc:

Subject:  Bioperl: Extracting genes from GenBank flat file



I am trying to develop an some perl script to extract the location of CDS or
genes in a DNA sequence based on the features described in the genbank flat
file.
I have two question:
- Has anyone ever tried such things before? I haven't found anything browsing
through the mail archive.
- I use Bio::DB::GenBank to download a sequence from genbank, now I was
wondering if the features in the genbank description are also downloaded and
stored somewhere. I thought I could use the annotation object to extract this
information but this seems not to be the case.
I use something like this:
$seq = $gb->get_Seq_by_acc($Accn[$i]);
$ann = $seq->annotation();
print $ann->description();

But then $ann->description() seems to be an empty string.
So now I not sure how to use theses objects anymore.

Has anyone some advice for me?

Thanks,
Gert Thijs


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+ Gert Thijs              gert.thijs@esat.kuleuven.ac.be +
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