Summary of DNA Binding Factor Database Query

Department of Molecular Karma YABLONSKY at BIOVAX.RUTGERS.EDU
Fri Aug 10 14:40:00 EST 1990


Thanks to everone!!!  I recieved much more of a response than I expected.
Below is the summary of the messages edited for relevance.  If you are 
interested, please read the references listed in the messages before 
contacting the senders.  This summary is of responses from both Info-GCG
and Bionet readers.  


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From:	IN%"SEQTEST at WCCF.MIT.EDU" 23-JUL-1990 12:13:03.44
To:	yablonsky at biovax.rutgers.edu
CC:	
Subj:	on sites for sticky things

Hi Michael,

	No I cannot answer your question, but you may be interested in Philipp
Bucher's article in J Mol Biol, 212, 563-578 which looks as though it might
help you. It has no email address, but is GCG compatible. Obviously its 
reference to the eukaryotic promotor database is relevant, but I do not know
if this can be obtained from the Netserver at embl.
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EPD and the EDP manual is available from the EMBL server  -MDY-
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	I'd be interested if you get a sensible set of replies - maybe 
summarise them and send them back to to the network?

	Regards,   Jasper Rees

	Seqtest at MITWCCF.MIT.EDU


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From: gad yagil IN%"LCYAGIL at WEIZMANN.BITNET"
Subject: binding sites
To: yablonski at biovax.rutgers.edu

Try Philipp Bucher, now at stanford (PHILIPP at GNOMIC.STANFORD.EDU).
See Bucher and Trifonov, nucleic acid research, 14: 10009 (86).

good luck.


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From:	IN%"ghosh at nexus.nlm.nih.gov" 23-JUL-1990 15:39:34.64
To:	yablonsky at biovax.rutgers.edu
CC:	
Subj:	gcg binding sites file


I have such a file, but it includes other sequences besides Drosophila. For
background you may want to look at a paper published in NAR 18.7:  1749-56.
Also I can easily create a subset of the file containing only sequences
from Drosophila.

- Dave G


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From:	IN%"dxp%trna at LANL.GOV" 23-JUL-1990 16:30:18.95
To:	yablonsky at biovax.rutgers.edu
CC:	dxp%trna at LANL.GOV
Subj:	transc. factor database


Michael,

I am answering your request on the GCG net request for a transcription factor
database.
I have developed an IBM compatable program that I have released that looks for
TF's in a sequence using a list file of TF binding sites.  I also have a unix
version available.  The 'Signal Scan' program is not GCG compatible, but you
may be interested in the list files of transcription factors.  

Let me know if you are interested in Signal Scan.  Also, if you find others
developing a transcription factor database or search programs, please let 
me know.

thanks

Dan S. Prestridge
DXP%LIFE at LANL.GOV
Theoretical Biology and Biophysics Group
T-10, MS K710
Los Alamos National Laboratory
Los Alamos, NM 87545

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From:	IN%"ghosh at nexus.nlm.nih.gov" 30-JUL-1990 18:32:03.05
To:	YABLONSKY at mbcl.rutgers.edu
CC:	
Subj:	TFD

There are at this time two mechanisms for obtaining a copy of TFD 
     (Transcription Factor Database), release 1.0:


(1)  Anonymous ftp:
	If you ftp into the account "ncbi.nlm.nih.gov" and enter "anonymous"
	as your login name, then anything (preferably your name) as the
	password, you will be in the NCBI repository.  From here if you
	enter the command "cd repository/TFD" you will be in the TFD
	anonymous ftp directory, where the primary TFD data files are located.
	For UWGCG users, some GCG-compatible files are located in the "gcgs"
	subdirectory of the TFD directory.

(2)  Floppy diskettes:
	Send a sufficient number of formatted floppy diskettes (in a 
	conventional format such as DOS, MacIntosh, UNIX, etc.) to hold
	1.2 megabytes of data, along with a self-addressed stamped diskette
	mailer to:

	David Ghosh
	National Center for Biotechnology Information
	NLM, NIH, Bldg 38A
	8600 Rockville Pike
	Bethesda, MD  20894



David Ghosh, NCBI
National Institutes of Health, USA

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Thanks again to everyone!!!  What a net!!  

 Michael D. Yablonsky                   internet: yablonsky at mbcl.rutgers.edu
 			                at&tnet: (908) 932-3052
 Waksman Institute
 Rutgers University                    A good planet is hard to find!
 Piscataway, NJ, 08854-0759





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