[Bioperl-l] Re: Promoter
Mon, 19 Feb 2001 00:50:23 +0000
Elia Stupka wrote:
> > hard). So I would suggest to keep these elements separate from the
> > promoter.
> I would argue the opposite, I would argue that we should be elastic even
> if perhpas inexact n biological sense (considering that the promoter field
> of science is prety inexact in itself).
> In other words, I think that promoter should be basically a SeqFeature
> container, so that at will people can implement SeqFeature compliant
> objects with more or less complexity, to describe their favourite promoter
> elements, and whatever complex behaviour they want to attrbiute to those
> elements. Whether the element is 10Kb upstream or not, I reckong it should
> be contained in the promoter object. In this way one can pull out from one
> object any information known about its regulatory elements.
> If this seems inapporpriate biologically we can argue at length about
> naming things,i.e. maybe it should be regulatory elements, or whatever, my
> point is that from the object point of view it would be nice to have
> everything in one object associated with the transcript.
> An obvious example of the usefuleness of this is if people want to start
> affing elements which are knwon to bind to each other and trigger
> something only if bound together. From a basic point of view, all you want
> is to ask what elements regulate this gene, and where are they? The other
> example being that you add some basic promoter element, then you discover
> a very strong enhancer 20Kb upstream, and just because we have a rigid
> object layer, we cannot simply say there is also this enhancer
> hmm... hope that was clear enough....
> Bioperl-l mailing list
I can see your line of thinking from the object method point of view. However
how this would handle the biological situation where an enhancer for one gene
is also the promoter for a second gene? (I have come across such a case in
Naming might be an issue - I might venture that you need to have a general
regulatory element class of which "promoter", "enhancer", "silencer",
might be subsets.
Does the binding of regulatory element to transcript in the method then
*require* that every regulatory
element have a transcript? Again there are cases where arbitrary DNA
sequences are tested
for regulatory activity where their target of action is either complex or the
gene is unknown.
Dr Samuel Aparicio BMBCh PhD | firstname.lastname@example.org
Wellcome Trust Centre for Molecular Mechanisms in Disease
Cambridge CB2 2XY. UK. | +44 1223 762663 (tel)