enhancer/promoter sequence

Peter Ashby p.r.ashby at dundee.MAPS.ac.uk
Wed Jun 13 11:48:12 EST 2001

In article <992449574.534353 at blaat.sara.nl>,
 "Frits" <aristaless at hotmail.com> wrote:

> Hi,
> What is currently supposed to be the best in silico way  to identify, or
> guess, regulatory sites, (potential) transcription factor binding sites,
> etcetera, when you find yourself staring at several kbs DNA that you know to
> have an important regulary potential in vertebrate gene regulation.
> Apparently the commercial software packages do not supply the means to do
> this.
> What are your favourite websites?


I wouldn't use it for 'several kb's of DNA' though. I would refine my 
search to small regions known by functional studies to be enhancers or 
promoters. The last time I did this on a 200bp region I got too many 
hits to handle. Part of the problem is that the binding sites for 
transcription factors are poorly defined. They often consist of 4-6bp 
core region which may have redundancy, but require poorly defined 
flanking sequences to bind the factor. So use advisedly and confirm 
binding before relying on an id.


Peter Ashby
Wellcome Trust Biocentre
University of Dundee
Dundee, Scotland
Reverse the spam and remove to email me.

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