identifying TF seq.'s in a promoter

martin LEACH leach at bu.edu
Wed Oct 18 16:46:36 EST 1995


Use the GCG program....excerpt below:

Use the gcg findpatterns command to search a DNA sequence for
matches to the Transcription Factors Database (TFD).
(The tfd-site-search and regsearch commands are no longer used.)

NOTE:   To use any gcg command you must first have typed gcg once after
logging
        in to the system.  Example:
        mbcrr% gcg
        (If you forget to type gcg you'll get the message "Command not
found.")
        The gcg package runs on mbcrr, darcy, and mbcrrc.
        For more information on findpatterns, type "genhelp findpatterns".

#------------------------------------------------------------------------------
# Usage:            findpatterns  -data=genmoredata:tfsites.dat
#
# DATA:                 File containing patterns.
#
# NOTE:  When you see the prompt "FINDPATTERNS in what sequence(s) ?"
# you must enter a DNA sequence filename in GCG format.
# Use readseq to convert your sequence to GCG format.
# Type "man readseq" for instructions.
#------------------------------------------------------------------------------

this is what I use on my system...it looks up matches with the tfsites.dat
file..

Martin

Ron Herzig (r-herzig at nwu.edu) 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

--
.....          Martin Leach                Email:leach at bu.edu 
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