[Bioperl-l] Re: Promoter

[Elia Stupka]

> 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
upstream...

hmm... hope that was clear enough....

Elia