YABLONSKY@BIOVAX.RUTGERS.EDU (Department of Molecular Karma) (08/11/90)
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@WCCF.MIT.EDU" 23-JUL-1990 12:13:03.44
To: yablonsky@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@MITWCCF.MIT.EDU
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From: gad yagil IN%"LCYAGIL@WEIZMANN.BITNET"
Subject: binding sites
To: yablonski@biovax.rutgers.edu
Try Philipp Bucher, now at stanford (PHILIPP@GNOMIC.STANFORD.EDU).
See Bucher and Trifonov, nucleic acid research, 14: 10009 (86).
good luck.
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From: IN%"ghosh@nexus.nlm.nih.gov" 23-JUL-1990 15:39:34.64
To: yablonsky@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@LANL.GOV" 23-JUL-1990 16:30:18.95
To: yablonsky@biovax.rutgers.edu
CC: dxp%trna@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@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@nexus.nlm.nih.gov" 30-JUL-1990 18:32:03.05
To: YABLONSKY@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@mbcl.rutgers.edu
at&tnet: (908) 932-3052
Waksman Institute
Rutgers University A good planet is hard to find!
Piscataway, NJ, 08854-0759