[Bioperl-l] getting DNA sequence for exon features from GFF

[Chris Fields]

On Aug 26, 2010, at 11:22 AM, kanmani radha wrote:

> Hi Everyone,
> 
> Thanks very much for this clarification.  Thanks a ton for every one who
> spared their time to educate me.
> 
> I see your points.  Please correct me if I am wrong.
> 
> I understand that, Its better to use use Bio::DB::SeqFeature or Bio::DB::GFF
> to load the fasta sequences (from a separate multifasta) file and
> then Bio::Tools::GFF to parse the feature info from a gff file . Then query
> the created database for the relevent GFF coordinates....
> 
> I will implement this.
> 
> Thanks once again.
> Kanmani

Yes, in general.  I forgot to mention that you can have an in-memory database as well, but it's only suggested if you have a few thousand or so features and small sequences (I think bacterial chromosomes will work).  

chris