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>,
IZZY7KI at MVS.OAC.UCLA.EDU wrote:
>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
>UCLA
>
    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!
    Tracy



More information about the Methods mailing list