I m trying to align different sequences of length not greater than 50 bp. Could I incorporate additional information such as stacking energy, entropy, bonds etc as additional criteria in the alignment?

The sequences are very similar.

  • $\begingroup$ Welcome to the site. Did you some literature review? Which bonds are you referring to? Bonds between each pair of sequences? Or bonds within a sequence? I think it would be clearer if you explain what is your goal (and maybe it provides some key words to help find more information). $\endgroup$ – llrs Jul 25 '18 at 8:43

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