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Promoter analysis

Tracy Aquilla aquilla at salus.med.uvm.edu
Fri Jul 29 16:05:50 EST 1994

In Article <19940725114727IZZY7KI at MVS.OAC.UCLA.EDU>,
>I am currently studying the regulation of several mammalian (mouse
>and human) promoters.  Of obvious interest are known transcription
>factor binding sites.  Since I wouldn't know an AP-1 site from an
>EcoRI site, I was hoping there might be a computer program on the
>net that would analyze a submitted sequence for consensus recognition
>sites.  Does anyone out there have any advice?  At this point, even
>a simple list of known consensus sites would be better than nothing.
>Thanks in advance,
>Benjamin S. Braun
    Check out TFD (transcription factor database) at NCBI. There is a HUGE
file of DNA consensus sites and many other supporting files there. Point
your terminal/PC to the FTP server at ncbi.nlm.nih.gov then change
directories to /repository/TFD. The SITES datasets (in the datasets dir.)
are provided in many different formats, such as: GCG, FASTA, MacVector, etc.
Peptide sequences can also be searched using the BLAST email server at NCBI.
You may also want to read NAR 20 (1): 3-26, "Compilation of
vertebrate-encoded transcription factors" by Steffen Faisst and Silke Meyer.
This lists many DNAbps and the sequences they recognize, as well as references.
Hope this helps some. Good luck!

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