promoter sequence listings

Michael Holloway ca566 at cleveland.Freenet.Edu
Sat Aug 15 21:09:43 EST 1992


In a previous article, DMEIER at mis.mcw.edu () says:

>Enter your message below. Press CTRL/Z when complete, or CTRL/C to quit:
>Hello all,  Can you help me?  I am looking for a listing of eukarotic promoter
>sequences.  For example, although estrogen response elements are similar, a
>number of bona fide EREs have been identified which differ at specific bases.
>Is there a list that has all the permutations of EREs, and other elements?      Thanks mucho in advance.       ...Dan Meier, DMEIER at mis.mcw.edu
>
By now you must be deluged in responses but I'll repeat the obvious one
anyway and throw in a couple of journal references that others may not have
given.  By far the easiest, and most extensive, way of getting what you
want is to ftp to ncbi.nlm.nih.gov, the NIH archives, and download the TFD
and EPD databases.  If you're lucky enough to have access to a Unix box,
there's even software for using the darn things to their full extent (I am
not so fortunate).
References:
David Ghosh, New developments of a Transcription Factors Database, 1990, TIBS
16:445-447.
	-Previous Ghosh references are sited. You may have even been 
	contacted by him by now.
Edgar Wingender, Compilation of transcription regulating proteins, 1988 NAR
16:1879-1903.
	-I seem to recall that this fella was also making a database but I
	can't recall the particulars at the moment.
J.Locker and G.Buzard, A dictionary of transcription control sequences,
1990, DNA Sequence-J. DNA Sequencing and Mapping 1:3-11
	-Interesting in that the authors set out to limit their list to
	just vertebrates and pol II promoters.

If you're scanning a sequence I can recommend the GCG similarity search
programs.  They're arkward to use, frustrating sometimes, but they get the
job done.

Warning: Do not, under any circumstances, start typing in your own
database.  It will take you much longer than you can imagine.  Use what's
out there already.

Mike
-- 
E-mail: mhollowa at ccmail.sunysb.edu (mail to freenet is forwarded)
phone:  (516)444-3612
I would claim to speak for my university but no one is likely to
believe it.



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