identifying TF seq.'s in a promoter

Jon Nakamoto jnakamot at ucla.edu
Sun Oct 15 02:49:09 EST 1995


Dear Ron,

Do you have access to a Macintosh running MacVector? If so, TFD
(Transcription Factor Database), which I'm sure you know about (I download
my files via the Hopkins BioGopher) actually has the complete list of
consensus sequences in MacVector format (I'm sure there are other formats,
although I wouldn't know how to use them). I downloaded the TF database
file, took a promoter sequence directly off GenBank, walked the disk over
to the lab next door running MacVector, performed a subsequence search
(you can specify # of allowable mismatches) and in several minutes got a
47-page single-spaced printout of potential consensus sequences (the
subsequence file originally supplied with MacVector only came up with 8
pages). Pretty amazing. 

Jon Nakamoto, MD
UCLA Medical Center
Pediatrics/Endocrinology
work e-mail address: jnakamot at pediatrics.medsch.ucla.edu


In article <45ptta$h7e at news.acns.nwu.edu>, r-herzig at nwu.edu (Ron Herzig) wrote:

> Bionetters,
>         We have recently cloned a gene and its promoter.  Given today's
> computer technologies, does anyone know a way to search the promoter 
> sequence for all potential consensus sequences it may contain using a 
> database of characterized transcription factors and the sites they bind.  
> It would be necessary to allow for a few mismatches as well.  Any suggestions 
> would be appreciated.  Please include enough detail for me to figure out 
> exactly what you're recommending.  Please respond by e-mail if at all
possible.
>         Thank you in advance.
> 
> Ron Herzig
> Northwestern University, Evanston, IL.   USA
> Department of Cell and Molecular Biology
> r-herzig at nwu.edu

-- 
Jon Nakamoto
jnakamot at ucla.edu



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