promotor and database-search?

Dan Jacobson danj at welchgate.welch.jhu.edu
Fri Jan 29 11:14:22 EST 1993


In article <1993Jan27.182937.12863 at gserv1.dl.ac.uk> HABERMANN at AIMP.UNA.AC.AT writes:
>To the EMBL-DATABANK,  bionet.molbio.embldatabank
>
>Suppose you had promotor sequences of several - functionally related - genes with a conserved sequence 
>motif in common, 
>1) how could you find out, if there is already a binding protein known for this specific motif?
>2) how would you look for promotors of other genes containing the same conserved sequence element?
>I know that there exists an Eukaryotic Promotor Database - somewhere out there - which might even be 
>useful. I also heard that this EPD is available on the EMBL-server. Is there any possibility to access this 
>database? If yes, how?
>If you have any ideas how to solve this problem - apart from performing a fasta with this sequence and 
>looking through the tons of output-datas by hand, we had this idea already and are not thrilled with the 
>thougt, since a fasta-search of about 20 nucleotides against the GenEMBL database overwhelms our 
>imagination - please let me know!
>Thanks in advance
>Bianca
>
>-----------------------------------------------------------------------------------------------------------------
>
>e-mail address (bitnet) :
>habermann at aimp.una.ac.at
>institute of molecular pathology,  Dr.Bohrgasse7, A1030 Wien
>
>_________________________________________________________________________________


Yes, there is an Euk. Promoter Database (EPD) and you can access it
by a variety of ways.  If you would like to search the database for
keywords or phrases you can search it by gopher. (If you don't know
what gopher is write me a note and I'll send you all the information
that you need to get it - it's free and on the net). 

In order to search the EPD Sequence database for keywords point
your gopher at merlot.welch.jhu.edu and go to the following
directory:

-->  12. Search Databases at Welchlab (Cloning Vectors, Euk. Promoters, NRL../

and in that directory read the About-these-searches file and then select

      -->  4.  EPD - Eukaryotic Promoter Database <?>

And now search for whatever keywords you'd like - for example
to retrieve all the entries on the promoters for heatshock proteins 
search for

heatshock

to search for all the promoters for heatshock proteins in Drosophila
search for

heatshock and drosophila


and so on....


If you'd like to retrieve the entire database and use it
for a fasta search go back to the top directory and select
the following directory:

 -->  2.  FTP Sites For Biology/

and then

      -->  22. NCBI Repository FTP Archive /

and then

           -->  5.  EPD/

and then

                -->  4.  db/

then just select the sequence database:

 -->  5.  epd33.seq.

and it will bring it to your system.  

It's already in Fasta format so just search your promoters
against it. 

Alternately you can retrieve the epd sequence database by
anonymous ftp from ncbi.nlm.nih.gov in the /repository/EPD/db/
directory.


Best of luck,

Dan Jacobson

danj at welchgate.welch.jhu.edu

Johns Hopkins University



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