[Bioperl-l] Bio::SeqFeature::GeneStructure and Prediction

Ewan Birney birney@ebi.ac.uk
Sun, 13 Aug 2000 17:55:16 +0100 (GMT)

On Wed, 2 Aug 2000, Hilmar Lapp wrote:

> James Gilbert wrote:
> > 
> > Hilmar,
> > 
> > I'd like to see the Ensembl Gene structure in
> > BioPerl, because I think it is more or less
> > correct.  In Ensembl a Gene has one or many
> > Transcripts, each of which can have a Translation,
> > and each Transcript has one or many Exons.
> > Transcripts share exons, and so you can get a
> > non-redundant list of exons from a gene.  So I'd
> > like to see a Transcript layer in there somewhere.
> > 
> I've already explained that to Ewan yesterday. A transcript is beyond the
> scope of this class. The GeneStructure is merely a representation of a gene
> structure or its elements as a feature with subfeatures, not more, not less.
> In particular, it is _not_ a Gene. It represents data, but it doesn't
> interprete them (mostly), and it is fairly independent from an underlying
> sequence object. One could add transcript features as sets of exon features
> though, but these will not be computed (how would you know?).

Now I am back from holiday I can comment on this:

I think Hilmar that you want to represent something which is closest in
Ensembl terms to "Transcript" (in fact, almost identical). I'd prefer not
to use the phrase "GeneStructure" here at all - it is going to lead to
tears as some people will expect to have Transcripts in Genes (indeed, I

My prefered name would be something like
Bio::SeqFeature::TranscriptionUnit or Transcript. 

I guess we can bash this out one-on-one over in SD. We must make sure we
meet up hilmar...

> A gene with transcripts would actually go into its separate class, as I think
> of it. So, there could be a Bio::Gene which, given a Sequence and a
> GeneStructure, may provide transcripts and information about alternative
> splicing.
> Maybe this needs more thinking.
> 	Hilmar
> -- 
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> Hilmar Lapp                                      email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics                   phone: +43 1 86634 631
> A-1235 Vienna                                      fax: +43 1 86634 727
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420