[Bioperl-l] GeneStructure & Promoter(s)

Hilmar Lapp hilmarl@yahoo.com
Mon, 19 Feb 2001 00:45:59 -0800

Ewan Birney wrote:
> On Sun, 18 Feb 2001, Hilmar Lapp wrote:
> >
> > In practice this means the following:
> > 1) We have to decide now whether to return an array or a scalar in
> > promoters(). My point was that Ensembl re-implements anyway, and
> > can enforce in the implementation that only a single promoter
> > feature be added. Is this okay with everyone?
> Who *wants* more than one promoter per transcript? 

A gene prediction result with suboptimal predictions included
(which BTW would also include overlapping exons; purely
biologically you would also disallow this, wouldn't you). Sorry,
that's my use case in this respect, and I want the model to cover

> > 3) We better decide now whether to add a property
> > regulatory_elements(), returning e.g. a GeneRegulatorI object. BTW
> > this could then also be the object returned by promoters(). A
> > related question is then also what distinguishes promoters() from
> > regulatory_elements().
> >
> This is not such a bad idea.

Thanks Ewan :-)) I've waited for this for months, you saved my day

> I guess regulatory_elements in my view would
> be on the gene (not the Transcript). But this is serious "no one really
> knows what is going on" terroritory. It would not kill me if we did not do
> this at all...

Quite encouraging. I'll wait and hear what other Ensembl folks
like to think before I dump the idea. (BTW I agree for gene
instead of transcript.)


Hilmar Lapp                              email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757