Identifying the Target from RNA Structure Ensemble
This Demonstration shows the ensemble tree, a hierarchical bi-partition of the ensemble of structures. The tree is sample output from the Wolfram Mathematica package RNAStructureIdentifier .
We focus on how to identify a target from a Boltzmann ensemble of secondary structures. The key idea is to employ an information-theoretic approach to solve the problem as a variant of the Rényi–Ulam game. The ensemble tree is constructed by recursively querying about whether or not a base pair of maximum information entropy is contained in the target. These queries are answered by relating local with global chemical probing data, employing the modularity in RNA secondary structures (see References).