Alignment using secondary and tertiary features of DNA to make similarity matrix

Question

[goonerrn]

I m trying to align different sequences of length not greater than 50. Is there any way to incorporate other information such as stacking energy, entropy, bonds etc. If there any way to align sequences(which are very similar) using such information? And possibly obtain a similarity matrix.

[Joe]

You might be interested in looking at HMMs through the HHSuite or HMMER. They don’t exactly carry the info you are after about energies etc, but they do calculate alignments based on secondary structures which might incorporate some of the info you need.