[Bioperl-l] Intron and exon information

[Hilmar Lapp]

Yes. Fixed. -hilmar

> -----Original Message-----
> From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
> Sent: Friday, June 14, 2002 12:54 PM
> To: Hilmar Lapp
> Cc: bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] Intron and exon information
> 
> 
> sure - just not sure where we uc/lc them - hopefully in the 
> gcg.pm code?
> Should be a simple fix if that is the case.
> 
> On Fri, 14 Jun 2002, Hilmar Lapp wrote:
> 
> >
> >
> > > -----Original Message-----
> > > From: Lars G. T. Jorgensen [mailto:larsj@diku.dk]
> > > Sent: Friday, June 14, 2002 8:14 AM
> > > To: bioperl-l@bioperl.org
> > > Subject: Re: [Bioperl-l] Intron and exon information
> > >
> > >
> > > "David Block" <dblock@gnf.org> writes:
> > >
> > > > This is kind of in my area - although I've been stuck in
> > > Java-land for a while.
> > > >
> > > > These 'files' of yours - what format are they in - just FASTA?
> > >
> > > The datafiles are outputs from the GCG suite. The Seq 
> object accepts
> > > the sequences so thats fine. But, they use casing for representing
> > > exons/introns and the SeqIO::gcg throws this information away.
> > >
> > > So I was thinking about patching the parser, but I don't 
> know if that
> > > is against the Design to let the SeqIO add features to a 
> Seq object.
> >
> > Sure that's fine, generally speaking. Case should actually 
> be kept by the parsers, to me the fact that gcg.pm doesn't is 
> a bug. Core guys, who disagrees?
> >
> > If case is kept you can just post-process the seq object 
> and attach features derived from the changes of case in the 
> sequence, e.g. along what Dave suggested, right?
> >
> > 	-hilmar
> > >
> > > But I think GCG can do FASTA output. Does this contain information
> > > about introns?
> > >
> > > BTW. Is there a printable class diagram somewhere. We 
> don't have a A0
> > > printer here...
> > >
> > > >
> > > > The alignments are done, right?  So what you need to do is
> > > figure out where the introns are, and then deduce the phase?
> > > >
> > > > You're going to have to create a
> > > Bio::SeqFeature::GeneStructure::Gene object, and use its
> > > intron capabilities.  Take a look at the perldoc for that
> > > module, see if you can shoehorn your data into there, and
> > > then I think Hilmar's excellent work will give you the 
> intron data.
> > > >
> > > > Let us know if this helps.
> > >
> > > --
> > > Mvh|Regards, Lars
> > > System administrator     | Student
> > > Bioinformatics Centre    | Department of Computer Science
> > > University of Copenhagen | University of Copenhagen
> > > http://www.binf.ku.dk    | http://www.diku.dk
> > > When's the last time you used duct tape on a duct? -- Larry Wall
> > >
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> 
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
>