enhancer/promoter sequence

Austin So (Hae-Jin) haejin at netinfo.ubc.caX
Wed Jun 13 12:41:46 EST 2001


There is no "best way". And the better ways require that some functional
information about the downstream gene exists, or that you have a database of
genes with similar expression profiles (read: microarrays or SAGE).

If you have the latter information at your disposal, then there are a few
ways to look at it, but I would probably start off with George Church's
"AlignACE", which has been applied to DNA and protein, and seems to be one
of the better one's out there...

http://arep.med.harvard.edu/

Otherwise, it is a complete crapshoot...lots of benchwork required...

"Peter Ashby" <p.r.ashby at dundee.MAPS.ac.uk> wrote in message
news:p.r.ashby-3A32F6.17481213062001 at dux.dundee.ac.uk...
> 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.

--
---
Austin P. So (Hae Jin)

I.I.S.G.P.
Biotechnology Laboratory
University of British Columbia

E-mail: haejin at netinfo.ubc.ca
http://server1.biotech.ubc.ca/~austin/index.html (updated 06/11/2001)






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