[Bioperl-l] Intron and exon information

[Jason Stajich]

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