[Bioperl-l] How to retrieve introns / exons from EMBL?

[Ole Schulz-Trieglaff]

Ups, I'm sorry, you're right. Stupid mistake. 
But thank you for your help.

Ole


On Sat, 2003-06-14 at 15:09, Jason Stajich wrote:
> The accessions you are using are mRNA so they won't have exons since the
> introns are already spliced out.  The should have CDS regions which is
> the coding region and may also have a 'gene' field which would
> encompass any UTRs, CDSes, and poly-A sites.
> 
> Try this accession, X55887.1 for an annotated genomic region which has
> exons.
> 
> Notice that accession L15409 doesn't even have any annotation.
> 
> -jason
> 
> On Sat, 14 Jun 2003, Ole Schulz-Trieglaff wrote:
> 
> > I tried several accession numbers like: D86967, L15409, AF169284 and
> > many more. But none of these entries carries an "exon" feature. This
> > seems strange to me. Are the informations about exon/introns saved in a
> > different way in EMBL ?
> >
> > Ole
> >
> > On Fri, 2003-06-13 at 19:36, Jason Stajich wrote:
> > > What accession number are you trying for, so we can test it too...
> > >
> > > On Fri, 13 Jun 2003 ole.st at gmx.de wrote:
> > >
> > > > Brian,
> > > >
> > > > I just read the point Q5.2 in the FAQ about retrieving all the features from
> > > > a
> > > > sequence. (was this the question you mentioned ?)  I used the sample code
> > > > to browse some entries of EMBL, but it doesn't work: I don't get any
> > > > features
> > > > with a primary tag like "exon" as described in the FAQ.  My perl program
> > > > looks like
> > > > this:
> > > >
> > > > $EMBL = new Bio::DB::EMBL->new();
> > > > $seq = $EMBL->get_Seq_by_id($id);
> > > > @genes = grep {$_->primary_tag eq 'exon' } $seq->all_SeqFeatures();
> > > >
> > > > foreach $exon ( @genes) {
> > > > print "Exon!\n";
> > > > }
> > > >
> > > > I've got no idea why it doesn't work.
> > > >
> > > > Ole
> > > >
> > > > > Ole,
> > > > >
> > > > > There is a question and answer in the FAQ about this, but I don't know if
> > > > > it's sufficient. Why don't you take a look and tell us if you need
> > > > > additional information. Certainly not a stupid question.
> > > > >
> > > > > Brian O.
> > > > >
> > > > > -----Original Message-----
> > > > > From: bioperl-l-bounces at portal.open-bio.org
> > > > > [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Ole
> > > > > Schulz-Trieglaff
> > > > > Sent: Friday, June 13, 2003 11:05 AM
> > > > > To: bioperl-l at portal.open-bio.org
> > > > > Subject: [Bioperl-l] How to retrieve introns / exons from EMBL?
> > > > >
> > > > > Hello,
> > > > >
> > > > > I'm a bioperl beginner and I apologize if this is a rather stupid
> > > > > question. But I'm looking for an easy method to extract the introns/exons
> > > > > of an EMBL-Entry with the start and stop position. I read the
> > > > > documentation of the Seq/LiveSeq classes but it is rather short and
> > > > > difficult to understand.
> > > > >
> > > > >
> > > > > Thank you very much,
> > > > >
> > > > > Ole Schulz-Trieglaff
> > > > >
> > > > > Berlin, Germany
> > > > >
> > > > > _______________________________________________
> > > > > Bioperl-l mailing list
> > > > > Bioperl-l at portal.open-bio.org
> > > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > > > >
> > > > >
> > > >
> > > >
> > >
> > > --
> > > Jason Stajich
> > > Duke University
> > > jason at cgt.mc.duke.edu
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> >
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> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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