A user approached me the other day with the problem
of desiging an antisense oligo to discriminate
between two related sequences.
I aligned the two sequences and I see regions
of mismatch, but I do not immediately see how to
quantify/rank the mismatch regions in say kcal/mol.
I was given a reprint which refers to a HUSAR program
called "foldsplit". Foldsplit may be of some use in selecting
regions for antisense design. Foldsplit appears to be
based on Mfold. I am trying to locate and if possible
obtain foldsplit for our local use. The HUSAR web site
is not very informative regarding foldsplit.
Would any of you care to share your thoughts on
antisense oligo design within existing GCG/EGCG