[Bioperl-l] Re: Gene Interfaces in Bioperl 0.7; Review of bioperl 0.7 from Ensembl

Peter Sterk sterk@ebi.ac.uk
Sat, 17 Feb 2001 15:30:34 +0000 (GMT)

On Sat, 17 Feb 2001, Ewan Birney wrote:

> My only comment is that I would expect 
> $transcript->promoter 
> to return a single object. A transcript is, in my view, defined to have a
> single promoter (ie, there is one unique starting point in the DNA). Of
> course, this really depends what on earth is "a promoter" --- which we are
> punting on right?

With one starting point, you probably mean the RNA polymerase binding site
(the promoter). Actual transcription start sites do vary. But yes, one
would expect a single promoter for a (primary) transcript. That is not to
say that a gene (another term that is difficult to define precisely) can't
have more than one promoter, but that would result in different
primary transcripts (allowing e.g. tissue-specific expression). Anyway, 
that is not an issue here. Always a joy to try and describe biology in a
series of ones and zeros ;-) 

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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