[Bioperl-l] Intron and exon information

[Lars G. T. Jorgensen]

"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. 

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
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