Sequence comparison

[Bob Wildin, M.D.]

I did some of this a few years ago.  The best I found was to combine
dot-matrix comparisons with homology searches with non-default
parameters.  I used mostly GenePro software for PC.  Unfortunately,
this gave no indication of statistical importance, and one must still
do the wet-lab studies to see if there is any significance there. 
Overall, I found this approach to defining potential regulatory
sequences of little practical use.