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

kanmani radha kanmaninradha at gmail.com
Thu Aug 26 17:24:40 EDT 2010

Hi Chris and others,

For a brief amount time i could get away using Bio::DB::Fasta to index fasta
files and Bio::Tools::GFF to iterate thru GFF features. But, i hit the wall
again. Looks like sequential access of GFF featuers is not sufficient, I
want to have a random access to it. I see the only way to do that is by
using Bio::DB::GFF as suggested by Chris.

Here is my question. Is there any tutorial to configure Bioperl  or this
module in particular to work with MySQL/postgres. I will really appreciate

And thanks for all your help.

On Thu, Aug 26, 2010 at 10:08 AM, Chris Fields <cjfields at illinois.edu>wrote:

> 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

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