My name's Ondrej and I'm an honours student under Dr. Steve Barker at the
University of Queensland working on RNA secondary structures. I've
recently found a 131 bp region repeated almost perfectly in another part
of the gene.
I was wondering whether anyone might know of any software which will make
finding such repeats (of any size) easier. ideally the software would be
Unix or Macintosh based.
I'm also interested in finding a program which will find local homologies
BETWEEN sequences rather than full sequence alignments. I've tried using
Blast2blast in that hope without much success - it only found the obvious
homologies - I'd like to allow for some redundancy.
Any help would be appreciated.
Thank you and have a pleasant day.