Bioperl: Extracting genes from GenBank flat file

gert thijs
Tue, 06 Jun 2000 13:39:39 +0200

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
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?

Gert Thijs

+ Gert Thijs     +
+                                                        +
+ Dept. Elektrotechniek ESAT-SISTA                       +
+ Kardinaal Mercierlaan, 94                              +
+ B-3001 HEVERLEE  Belgium                               +
+ Tel :  +32-16-32 18 84 ---- Fax : +32-16-32 19 70      +
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