Promoter Analysis Program

Martin D. Leach leach at bu.edu
Thu Feb 9 11:05:36 EST 1995


In article <skuroda-0902952255340001 at 133.1.4.35>,
skuroda at inherit.biosig.kobe-u.ac.jp (Shun'ichi Kuroda) wrote:

> Dear Sirs:
> 
> I am an assistant professor of Kobe university.  
> Before the severve earthquake on Jan 17, I posted same question 
> to this NG.  But the RESs for my question could not be arrived at 
> our server, since the server was broken by the earthquake.
> So I repost the same question.
> 
> (Question)
> I have a novel promoter sequence from human genome, of which 
> length is about 2kbp and has enough transcriptional activity.  
> However, it has been still unclear whether the promoter sequence 
> contains known promoter motifs or not.  
> If the database of the known promoter motifs is available, it will 
> be helpful for us to construct the deletion mutants and understand 
> the essential transcriptional region of the promoter sequence.
> Therefore, I want to know the services for analyzing the promoter
> sequence, which are on internet or distributed as commercial 
> softwares. 
>  Any comments will be appreciated.
> Many thanks,
> 
Hi there

taking a look at the server I use....i see:

Use the gcg findpatterns command to search a DNA sequence for
matches to the Transcription Factors Database (TFD).
(The tfd-site-search and regsearch commands are no longer used.)

NOTE:   To use any gcg command you must first have typed gcg once after logging
        in to the system.  Example:
        mbcrr% gcg
        (If you forget to type gcg you'll get the message "Command not found.")
        The gcg package runs on (my server name deleted)
        For more information on findpatterns, type "genhelp findpatterns".

#------------------------------------------------------------------------------
# Usage:            findpatterns  -data=genmoredata:tfsites.dat
#
# DATA:                 File containing patterns.
#
# NOTE:  When you see the prompt "FINDPATTERNS in what sequence(s) ?"
# you must enter a DNA sequence filename in GCG format.
# Use readseq to convert your sequence to GCG format.
# Type "man readseq" for instructions.
#------------------------------------------------------------------------------


This is the Ghosh Transcription factor database (ver 5.0)



...this is taken from a http site


    Transcription Factor Database (SITES)
                           Release 6.3, March 3, 1993

David Ghosh
National Center for Biotechnology Information
NLM, NIH
Bethesda, MD  20894  USA

_____________________Gopher Specific About------------------------

The Transcription Factor Database Sites table has been reformatted into
the following format and indexed.

SiteID    S00064
Factors   Sp1                       
Site      Sp1 CS1                        
System    MAMM       
Sequence  KGGGCGGRRY                               
Reference Nature 316: 774-8 (1985)                          

Users should note that the searches for SEQUENCE matches to this
database can be done through gopher by using either:

a) The exact, entire sequence pattern as it appears in this database
(i.e. no expansion of IUPAC ambiguous codes).
e.g. KGGGCGGRRY

b) Using the partial word search option of this Gopher server
(.....the * wildcard can only be used to expand the "word" to the right).
e.g. KGGGCGG* 


The boolean operators "and", "or", and "not" are recognized as operators.
If no specific separator is used between multiple words the "or" opertor is 
assumed.

The Gopher software does not provide the ability to search for specific 
DNA or Protein sequence patterns within a dataset.


_____________________General Specific About------------------------

References:

The following references may be consulted for a background
and general description of this database:

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.

The following sources have been helpful in maintaining and 
updating portions of this database: 

Faisst, S., and S. Meyer (1992)  Nucleic Acids Research 20:  3-26.
Locker, J., and G. Buzard (1990)  DNA Sequence 1:  3-11.
Wingender, E. (1988)  Nucleic Acids Research 16:  1879-1902.

VI.  Help and further information:

The following addresses can be used for help requests, mailing
list requests and general questions:


Email (internet) address                Purpose
----------------------------------------------------------------------------

tfdhelp at ncbi.nlm.nih.gov                TFD-related technical help requests

tfdinfo at ncbi.nlm.nih.gov                Messages or questions addressed to
                                        the TFD users community

tfdinfo-request at ncbi.nlm.nih.gov        Requests for subscription to the
                                        TFDINFO users mailing list

.




.........

also check out

http://sun01.iigb.na.cnr.it/iigbBiol.html
http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html
http://kiwi.imgen.bcm.tmc.edu:8088/bio/bio_home.html


BCM seems the best starting point...although I believe you can only scan
DNA and protein sequences for matches to other DNA or proteins....at the
moment I dont believe their are any web sites for your type of service....

I used to perform TFD-search on my server which would identify consensus
sequences from an .IG format DNA file.....However, as I first
mentioned...this is now done using the GCG program and the findpattern
command...(more help on GCG is found on the launcher page at BCM.

Also...email to the TFD site as mentioned above...I think you can email
your sequence to that site and a search is performed..not sure
though...let me know if this works.....


ciao

Martin

-- 
.....          Martin Leach                Email:leach at bu.edu 
   _|____      Dept. of Pharmacology       Phone: (617) 638-5323        
   / o  /      Boston Univ. School of Med. Fax:   (617) 638-4329         
 _/  |-/__==/  80 E. Concord St. (L603)
(BULLDOZER) \_ Boston MA 02118            "Not the old underpants 
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p.s. try BioMOO  -virtual biology on the internet..
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