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:
> 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
> 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.
Wellcome Trust Biocentre
University of Dundee
Reverse the spam and remove to email me.
More information about the Methods