New approaches for promoter region analysis?

Alexandr Spirov spin at ief.spb.su
Mon May 29 11:16:18 EST 1995


          Dear Colleaguaes:
My request

>          Hello Everyone!
>  I am looking for software (rather then Dan Prestridge'
>  Signal Scan) which make more complicated analysis of
>  gene regulatory regions or non-coding DNA as a whole.
>  Particularly I am interesting in scaning, analysis
>  and comparisons of the clusters of the transcription
>  factors binding sites (such as regulatory sites in
>  Drosophilian even-skipped, rhomboid or Kruppel genes).
>       Alex.Spirov.

as well as similar question of Dr. Mark Lamkin
(Boston Unversity School of Graduate Dentistry):

> I am interested in comparing 5' sequence of genes for potential
> regulatory elements. Wondering if anyone has suggestions for freeware
> or shareware on Windows 3.1.

have a little response.
But I really thank Sean Higgins for Suzuki citations:

> Suzuki and Yagi.  1994.  PNAS  91:12357-12361.
> Suzuki  1994.  Structure  2:317-326.
> you will most likely find these more up to data and very interesting.


     What does it mean? That nobody know and
nobody use approaches for the gene regulatory
regions analysis another then simple
scanning of DNA sequences to find signal sites from
Ghosh's Transcription Factor DataBase (such as SIGNAL SCAN
or SEQAID and some others)?
     However last year I have found email about
Sandia National Labs Workshop on COMPUTATIONAL MOLECULAR
BIOLOGY (June'1994, Albuquerque, NM)
with following report:
   Craig Benham (Mount Sinai School of Medicine)
  "New search strategies for DNA regulatory regions".
And this spring I received annoncement of
"BioInformatics & Genome Research" Conference (June'95,
Cambridge) with short summary of following report by
Ary L.Goldberger (Harvard Medical School):
  "Fractals, DNA, and Evolution of Biologic Complexity"
where he discussing differences between coding and non-
coding DNA sequences with positions of fractal
mathematics.
     Could anybody give citations on A.L.Goldberger and
C.Benham papers about discussing subject?
     Thanks,
          Alex.Spirov.

==================================================================
                       Alexander V.Spirov, PhD
 Sechenov Institute of Evolutionary Physiology and Biochemistry
                  Russian Academy of Sciences
           44 Torez Pr., 194223 St-Petersburg, Russia
       7 812 552 32 19 (phone)     7 812 552 30 12 (fax)
                   e- mail: spirov at ief.spb.su
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