[Bioperl-l] est2genome and bioperl

[Hilmar Lapp]

On Tuesday, October 1, 2002, at 11:03 AM, Jason Stajich wrote:

> Not yet - there is one in Ensembl we could probably lift - either way
> AFAIK this is a very trivial format to parse so would be very simple to
> write one.  Not sure how to handle multiple good hits in a segment in
> terms of stitching them into a gene - but again ensembl has 
> probably deal
> with this.
>
> We've not really fleshed out the Bio::SeqFeature::Exon,
> Bio::SeqFeature::Gene objects (Hilmar should these perhaps feed better
> with the Bio::Tools::Prediction::Exon objects or be combined?).
>

Bio::Tools::Prediction::Exon is-a Bio::SeqFeature::Gene::Exon, and 
hence readily fits into the Bio::SeqFeature::Gene objects 
(Transcript etc).

The other EST/cDNA/mRNA to genome alignment tool parsers (notably 
there is a sim4 parser, which may fit your bill as well) return 
Bio::Tools::Prediction::Gene objects.

	-hilmar
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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