Database of DNA binding sites

Harry Mangalam mangalam at uci.edu
Mon Oct 4 12:04:00 EST 1993


In article <CE88q6.LvL at biobase.aau.dk>, moreira at biobase.aau.dk (Jose
Moreira) wrote:
> 
> Hi netters,
> 
> I have a "small" problem.
> I need to search a yeast DNA sequence for known binding motifs,
> as thoroughly as possible.
> That means I would like to know where and how I can do such 
> a search.
> 
> Thanks in advance
> 
> _________________________________________
> 
>  Jose' Moreira & Peter Schjerling
>  Dept. of Genetics, Univ. of Copenhagen

You didn't mention what platform you wanted to try but if you have access
to a unix (or even DOS)  machine, you could use the nice, fast "signalscan'
by Dan Prestridge.
 There's also an old very slow Mac version that's not supported anymore.

 Or if you don't, you mail me the sequence with the the database you'd like
to search (yeast, mammal, all eukaryotes, etc) and I'll run it for you and
return the output by mail (I just updated the Transcription Factor Database
tables a day ago for someone else).  

Here's the descriptive blurb.


                Prestridge, D.S. (1991) SIGNAL SCAN: A computer program
that
                scans DNA sequences for eukaryotic transcriptional
elements.
                CABIOS 7: 203-206



  SIGNAL SCAN is a program developed to facilitate the analysis of DNA
sequences for known eukaryotic signals.  This program is FREE. You may copy
and distribute this program, but you may not charge for its distribution.
You MUST register the program by sending your name and address to the below
address. Registering this program helps to justify the program for funding
purposes.  For registering the program you will automatically be notified
of
SIGNAL SCAN changes and updates. PLEASE REGISTER, you will help assure the
future of SIGNAL SCAN.
  The source code is written in the `C' language and is fairly easy to port
over to other hardware and operating systems.  The source code will be made
available upon request. You may make changes to the source code, but may
not
release the modified program or source code without my authorization.
  If you use this program in published research, please site:
Prestridge, D.S. (1991) SIGNAL SCAN: A computer program that scans DNA
sequences for eukaryotic transcriptional elements. CABIOS 7, 203-206.
  The author welcomes comments and suggestions on the program or additions
to the database.  Please contact:

  Dr. Dan S. Prestridge                        tele:(303) 465-0658
  Dept. of Mol., Cell., and Devl. Biology     
email:DANP at BEAGLE.COLORADO.EDU
  University of Colorado
  Boulder, Colorado   80309-0347

Cheers
hjm

Harry Mangalam, VCO/Micro+Mol Genetics, Irvine Hall, Coll of Med, UC
Irvine,
Irvine, CA, 92717, Vox:(714) 856-4824, Fax:(714) 725-2118, mangalam at uci.edu

There's no better glory, when it all gets harried, to be laughing in the
midst of it all.   --- Doug and the Slugs ---




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