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

[Jason Stajich]

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