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. ********************************************** 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. *************************************************************** EPD and the EDP manual is available from the EMBL server -MDY- *************************************************************** 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 ************************************************ 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. *********************************************** 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 ********************************************* 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 **************************************************** 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 *************************************************** 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