Inquiry regarding sequence analysis (esp promoters/enhancers)

t. linn tlinn at newshost.uwo.ca
Fri Aug 14 01:57:34 EST 1992


In article <1992Aug7.013257.12200 at u.washington.edu> rbradbur at hardy.u.washington.edu (Robert Bradbury) writes:

>   I am interested in obtaining opinions in two areas:
>
>     1) Are there databases which contain a list of the known promoter/enhancer
>	sequences for eukaryotes and/or is there software which can use this
>	information to identify these regions in a given sequence?  I would
>	prefer packages which are designed for this specific task rather than
>	a collection of GCG commands which will always be out of date given the
>	ever increasing number of promoter/enhancer sequences.
>
>    2) Could people send me brief notes regarding their experience with PC
>       (DOS or UNIX) based software packages for sequence analysis (scanning
>       CD-ROM databases, sequence comparisons, PCR primer and probe design, etc).
>       I'm interested in stand-alone systems which do not require large computers.
>       E-mail response is fine, I will post a summary for general reference.
>
>   Thanks,
>   Robert Bradbury		uunet!sftwks!bradbury or rbradbur at u.washington.edu
>

Check out David Ghosh's extensive TFD (Transcription Factors
Database), in particular the SITES table for the sequences of all(???) known
factor-binding sites (there are some 2036 entries!).  The database is
available from the National Center for Biotechnology Information
(NCBI) by FTP to NCBI.NLM.NIH.GOV in the 'repository' directory.  Also, a
couple of new email servers were just recently made available from
NCBI that should allow you to perform searches on this database: to find
out how they work just send an email message only containing the word HELP
to blast at ncbi.nlm.nih.gov and retrieve at ncbi.nlm.nih.gov.  The
publications describing this terrific piece of work are:

Ghosh, D. (1990)  Nucleic Acids Research 18:  1749-1756.
Ghosh, D. (1991)  Trends in Biochemical Sciences 16:  455-457.
Ghosh, D. (1992)  Nucleic Acids Research 20S:  2091-2093.

Also check out the EPD (Eukaryotic Promoter Database):
EPD -  Eukaryotic Promoter Database. A collection of biologically
functional, experimentally defined RNA POL II promoters active in
higher eukaryotes. Maintained by Philipp Bucher
(Philipp.Bucher at Isrec.Arcom.ch).       Last update: Dec. 17, 1991.

This is also available by FTP'ing to ncbi.nlm.nih.gov in the
'repository' directory.  I'm not as familiar with that DB so I can't
offer specifics.

Good luck!


Keith

--
Keith L. Steward                          Voice: 519 679-2111 ext.
6618 Dept. Microbiology & Immunology        Fax: 519 661-3499
Dental Sciences Bldg.                  Internet: KLSTEWARD at UWO.CA
University of Western Ontario
London, Ontario, Canada, N6A 5C1
--
--
Keith L. Steward                          Voice: 519 679-2111 ext. 6618
Dept. Microbiology & Immunology             Fax: 519 661-3499
Dental Sciences Bldg.                  Internet: KLSTEWARD at UWO.CA
University of Western Ontario
London, Ontario, Canada, N6A 5C1




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