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).