Most Informative Base Pairs (MIBPs)

Information theory characterization and visualization of RNA secondary structure using Boltzmann ensemble finds a small number of most informative base pairs (MIBPs) and their conflicting base pairs (if any) controls three levels of structure.

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LinearPartition shold do the probablilities part in near linear time.
They have a web server (beta).

Combined should be a fast way to get Most Informative Base Pairs (MIBPs) and their Conflicting Base Pairs so one can concentrate efforts on mutations that really matter.