Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.

ABSTRACT:

Background

The nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of the RNA secondary structure Boltzmann ensemble. However because a given RNA secondary structure only contains a fraction of the possible helices that could form from a given sequence, the Boltzmann ensemble is multimodal. Several methods exist for clustering structures and finding those modes. However less focus is given to exploring the underlying reasons for this multimodality: the presence of conflicting basepairs. Information theory, or more specifically mutual information, provides a method to identify those basepairs that are key to the secondary structure.

Results

To this end we find most informative basepairs and visualize the effect of these base

SUBMITTER: Lin L 

PROVIDER: S-EPMC5836418 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature