[Bioperl-l] Alignment optimization using degenerate code

[manni122]

I have a problem in programming, that once solved might be worth adding it to
the BioPerl bundle.
I want to pairwise align DNA sequences with as little gaps as possible. To
reach this I want to run a first round of alignment, than compare the
alignment pair and search for opposite codons that can be exchanged each
with another one coding for the corresponding amino acid. This should
increase their identity score.
Does anyone have an good idea how to start?
Appreciate any help with this!
Markus 
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