finding promoter sequence

Martin Leach leach at mbcrr.harvard.edu
Wed May 11 14:41:45 EST 1994


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 ?
> 
> Thanks in advance for your help.
> 
> Dave.

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


-- 

.....          Martin Leach                Email:leach at mbcrr.harvard.edu 
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