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Promoter elements Database????

Stephen R. Lasky Stephen_Lasky at brown.edu
Fri Feb 2 08:44:22 EST 1996

In article <310FF66A.A0A at ulam.generes.ca>, kalch <kalch at ulam.generes.ca> wrote:

> Hi,
> we are trying to "map" promoter elements from known DNA sequence.  
> However, we find that the DNA analysis programs we have in the lab 
> (MacVector and GeneWorks) are not suitable for this analysis.  Could 
> someone please post (or respond to me directly) where I can send (or 
> download) a program that will search for promoter elements (e.g. 
> Sp1, ERE, AP1, AP2, etc)?
> Thanks,
> Michael

MacVector does do this (I'm not saying that it does it well, but it has
the ability).  I think that the newer versions ship with a transcription
factor subsequence file that has over 600 sites bound by proteins in
promoter regions.  You just have to do a nucleic acid subsequence search. 
I ran a test against the junD promoter and it found all the sites that had
been mapped by Shaul etal when they cloned it (except the TATA box.  I'm
not sure why it didn't find that as one of the subsequences is exactly the
same sequence as the tata box in the junD promoter.  Sometimes the exact
base that the site starts at are off by 1 or two, but that's more
dependant on what you call a binding site rather than the prgms ability to
recognize it as one.

Standard disclaimers about not working for IBI etc.


Stephen R. Lasky Ph.D.   Brown U/Roger Williams Medical Center,  Providence, RI.   
Phone: 401-456-5672     Fax: 401-456-6569     e:mail: Stephen_Lasky at brown.edu
America may be unique in being a country which has leapt from barbarism to decadence without touching civilization.  John O'Hara.

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