Alignment on the basis of predicted 2ndary structure?

ketchup Ketchup at cris.com
Wed Dec 11 14:32:46 EST 1996

I may be mistaken, but I think there is a database, 3d-ali, at the 
embl that has lots of sequences aligned by secondary structure. Hope
this helps.


>   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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