finding promoter sequence

Lee F. FrankKolakowski lfk at receptor.mgh.harvard.edu
Wed May 11 19:38:42 EST 1994


On Wed, 11 May 1994 19:41:45 +0000,
leach at mbcrr.harvard.edu (Martin Leach) said:
> In article <2qr47b$lub at agate.berkeley.edu>, Theo at mendel.Berkeley.EDU (AT)
> wrote:
>> What is the best way (or computer program) to identify eukaryotic
>> (or mammalian) promoter(s) in a DNA sequence ?

> Search for euk transcriptional start consensus seqs, look for common
> TF sites , ccat boxes, tata boxes, shine delgano sequences. (I use
> MacVector from IBI). If u have these sites it is promising. Only
> test if prom by in vitro transcription (nuclear run-off). Or by
> transfection into cells - test for orientation specificity (are some
> exceptions eg. Murine DHFR gene promoter). Or look for Initiator
> sequences....

Martin and Theo,

I think what Theo wanted is a computer program to scan for TF sites in
his DNA sequences. There are several methods and programs to do this.

1) get Gosh's Transcription Factor Database (TFD) from some where like
   ncbi.nlm.nih.gov:repositiory/tfd or is it TFD. Use the GCG formated
  file with any of the GCG programs that find restriction sites.

2) get signal scan software from:
  Dr. Dan S. Prestridge                        tele:(303) 465-0658
  Dept. of Mol., Cell., and Devl. Biology      email:DANP at BEAGLE.COLORADO.EDU
  University of Colorado
  Boulder, Colorado   80309-0347

3) use Philipp Bucher's eukaryotic promoter database (EPD) with fasta
   from ncbi.nlm.nih.gov:repository/EPD.

One you have some idea of what your promoter might have in it, couple
the piece of DNA to a reporter gene (luciferase is good) and begin
you reporter bashing. There are lots of reports showing the results of
this kind of exercise in the literature.

Best wishes





                                        
-- 
Frank Kolakowski

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