Alignment on the basis of predicted 2ndary structure?

John Calley jnc at becker.biosci.arizona.edu
Tue Dec 10 12:36:51 EST 1996

   I would like to be able to align a bunch of sequences on the basis of
their secondary structure.  I have a set of sequences that I know are
related but I can only find a few isolated areas where the sequence
similarities are close enough to align them on that basis. When I do
a secondary structure prediction, on the other hand,  I can see some
clearer relationships. Ideally I'd like to have a program take both
secondary structure and primary structure into consideration in doing an
alignment but I'd settle for just secondary structure. Does anyone
have any suggesions?
   Thank you very much,
      John Calley

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