Help with searching promoter sequences for transcription factor recognition sequences

David Johnson Johnson at biomed.yale.edu
Thu Jul 27 15:16:37 EST 1995


In article <3v6imi$jqm at cwis-20.wayne.edu>, Anton Scott Goustin
<asg at cmb.biosci.wayne.edu> wrote:

> EILEEN <FURLON93 at IRLEARN.UCD.IE> wrote:
> 
> >Dear reader,
> >        If there is anybody reading this who knows a database or a good
software package, I would be very grateful for any info. yo=
> u could give me.
> 
> MacVector 4.5.2 (Kodak Imaging Technologies, Rochester, NY) does a nice
job searching a NA sequence for TF recognition motifs such a=
> s AP1 sites, SP1 sites, NFkappaB sites, CREB sites, etc.  The 4.5.2
version comes with a nice file of these motifs called:
> 
> TFDSITES.SUBSEQ.7.0.aa
> 
> This file not only has the sites, but literature references to where the
site is defined.  Very nice.
> 
> Problem:  the program MacVector costs alot (~$2,000)
_________________________
Colleagues,
   The TFDsites database is in the GCG (Genetics Computer Group) package
of DNA analysis programs, so you can scan DNA sequences for candidate
sites using this database with (I think) "findpatterns".  
   The only problem I encountered using GCG for this purpose was that one
must first "fetch" the TFDsites database into your own directory before
using it to search your DNA sequence.  (Maybe one can avoid this step if
you know how to tell the program where to find the database.)  
   For more info, there is a GCG newsgroup (and probably a few FAQs) and a
WWW page.  

best of luck,
-Dave



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