Bioperl-guts: repetitive DNA

Peter L. Schuerman schuermanp@missouri.edu
Wed, 8 Sep 1999 16:23:27 -0500


Dear Listmembers,

I'm interested in finding a way to search for repetitive DNA arrays 
in genomic sequence, and I was wondering if anyone had written a 
module for this purpose.  It's fairly simple to search for repeats, 
but I'm also interested in finding ones which are slightly imperfect 
--- a few insertions, a few deletions, a few substitutions, e.g.:

ATATATATATATAT (normal)
ATATATATTATAT (deletion of an A)
ATATATATCATATAT (insertion of a C)
ATATATGTATATAT (substitution of an A for a G)
ATATTATATAATATAT (insertion and deletion)
etc...

Is there a way to write a regular expression that is forgiving enough 
to pick up arrays with these sorts of imperfections?

Regards,
Peter L. Schuerman

Department of Biosciences
109 Tucker Hall
University of Missouri at Columbia
Columbia, MO 65211

office: schuermanp@missouri.edu           home: schuerman@biosci.org
      "Who walks with truth, generates life." - Sumerian proverb
=========== Bioperl Project Mailing List Message Footer =======
Project URL: http://bio.perl.org
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-guts.html
====================================================================