Searching for DNA binding sites

Harry Mangalam mangalam at
Thu Mar 7 20:26:42 EST 1996

In article <4hfur8$fv at>, mary at (Mary ) wrote:

> I would like to look for patterns/homologies within a 50 kb contiguous
> DNA sequence. I am looking for hints regarding a putative binding site.
> I don't have a very good idea what the site is but I can make some
> guesses. Can anyone tell me the best program for this purpose?
> Mary Fernandes

If by this you mean that you're looking for degenerate binding sites for a
family of transcription factors or other DNA binding proteins, you could
use Dan Prestridge's signalscan (which matches DNA sequence to the
transfac or transcription factor database):

To get the latest version, anon. ftp to, to directory
pub/sigscan/pc or pub/sigscan/unix.  If you need installation instuctions
or help, send Email to danp at

 or the GCG program FINDPATTERNS which you can use to describe ambiguous
binding sites, or even Wu and Manber's 'agrep' (a variation on the unix
utility 'grep') which does very much the same thing (and is free):

"Wu and Manber, "Fast Text Searching with Errors", Technical report
#91-11, Department of Computer Science, University of Arizona, June 1991."

If not, I don't understand your question.

Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine,
      Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598
  Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW 

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