StreAM-[... formula ...]: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs

In this work, we present a new coarse grained representation of RNA dynamics. It is based on adjacency matrices and their interactions patterns obtained from molecular dynamics simulations. RNA molecules are well-suited for this representation due to their composition which is mainly modular and assessable by the secondary structure alone. These interactions can be represented as adjacency matrices of k nucleotides. Based on those, we define transitions between states as changes in the adjacency matrices which form Markovian dynamics. The intense computational demand for deriving the transition probability matrices prompted us to develop StreAM-Tg, a stream-based algorithm for generating such Markov models of k-vertex adjacency matrices representing the RNA