identifying TF seq.'s in a promoter

martin LEACH leach at
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
        in to the system.  Example:
        mbcrr% gcg
        (If you forget to type gcg you'll get the message "Command not
        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 looks up matches with the tfsites.dat


Ron Herzig (r-herzig at 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

.....          Martin Leach                Email:leach at 
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