[Bioperl-l] retrieving gene model from gff database

Tobias Straub tobias.straub at lmu.de
Wed Oct 26 13:18:47 EDT 2005

dear all,

probably kind of a basic question but I'm somehow unable to answer it 
without help:

I have the most recent gadfly GFF database loaded. now I simply want to 
get the gene models for selected genes - like searching with 
get_feature_by_name(-class => "Gene", -name=>"Gene_of_interest") - and 
to find out whether they contain annotated introns or not.

first problem is that the class gene does not seem to be supported by 
the GFF database. do I need to use an aggregator for that? if I have to 
use an aggregator, how do I search for the gene then? so far I was only 
able to get the gene when searching for class 'Sequence'. but this 
won't yield a gene-structure then, right?

thank you in advance!

Dr. Tobias Straub         Adolf-Butenandt-Institute, Molecular Biology
tel: +49-89-2180 75 439         Schillerstr. 44, 80336 Munich, Germany

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