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?

http://transfac.gbf.de/

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

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




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