[Bioperl-l] Re: Promoter

[Peter Sterk]

On Sun, 18 Feb 2001, Ewan Birney wrote:

> I would claim quite strongly now that $transcript should have one and only
> one promoter (of course, a single gene can have many transcripts and
> therefore many promoters).

Agree.

> Quite what is inside a promoter object is, for the moment, unclear,
> perhaps 
> 
> $promoter->tata_binding; # seqfeature indicating tata binding region
>                          # undef if not defined/not there


 
> $promoter->transcription_factors # array of seqfeatures, type
>                                  # transcription factor...

That's a dangerous one, and really depends on what definition of a
promoter one wishes to use. Transcription factor binding sites are not 
necessarily located in the promoter region, they can be upstream and
downstream of the promoter, sometimes far away (DNA is not a
two-dimensional molecule after all, which makes studying these elements so
hard). So I would suggest to keep these elements separate from the
promoter. 

> 
> I think a transcript having more than one promoter should be split into
> two transcripts.

Definitely.

Peter

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Dr. Peter Sterk                                      Email: sterk@ebi.ac.uk
Genome Project Curator                               Tel  : +44 1223 494464
EMBL Nucleotide Sequence Database                    Fax  : +44 1223 494468

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