RNA secondary structure similarity identification

Peter Leif Bergsagel bergsage at helix.nih.gov
Thu Jan 13 14:16:10 EST 1994

I have the sequence of different stretches of RNA that bind to a protein. I
am trying to develop a consensus RNA binding site. I suspect that it is
related to the secondary (or tertiary) structure. When I plot these out
using FOLD I have a very hard time comparing one structure to another, yet
alone a whole series. Are there any suggestions for how to determine the
consensus site sequence ?

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