Help with searching promoter sequences for transcription factor

Mike Holloway mike.holloway at stjude.org
Thu Jul 27 13:47:57 EST 1995


In article <3v5svg$mcm at mserv1.dl.ac.uk>, EILEEN <FURLON93 at IRLEARN.UCD.IE> says:
>
>Dear reader,
>          I have been trying to identify a number of footprints that I have
>obtained using a very old software package, MacDynamic. Unfortuneately the
>database that this program is using is very old and a lot of newly identified
>transcription factor recognition sequences are not in it.

You really have to look up the references and read about TFD before proceeding 
further.

Ghosh, D. (1990)  Nucleic Acids Research 18:  1749-1756.
Ghosh, D. (1991)  Trends in Biochemical Sciences 16:  455-457.
Ghosh, D. (1992)  Nucleic Acids Research 20S:  2091-2093.

Be sure to cite him in any publication.  It will ensure his continued interest. 
The sites database is up to (at least) version 7.  You can download it from NCBI. 
It would be pretty silly if MacDynamic didn't allow you to install an update; 
but then I've seen some pretty silly things on Macs.  If you can't use the new 
sites list there is at least one public domain search program that uses TFD:

Prestridge, D.S. (1991) SIGNAL SCAN: A computer program that scans DNA 
sequences for eukaryotic transcriptional elements. CABIOS 7, 203-206.

I've used it on a DOS system.  Not certain if a Mac version is available.  

The TFD files at NCBI will have a version formatted to work with the GCG search 
programs.

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