α-HMM: A Graphical Model for RNA Folding
Sixiang Zhang Aaron J. Yang Liming Cai
RNA secondary structure is modeled with the novel arbitrary-order hidden
Markov model ({\alpha}-HMM). The {\alpha}-HMM extends over the traditional HMM
with capability to model stochastic events that may be in influenced by
historically distant ones, making it suitable to account for long-range
canonical base pairings between nucleotides, which constitute the RNA secondary
structure. Unlike previous heavy-weight extensions over HMM, the {\alpha}-HMM
has the flexibility to apply restrictions on how one event may influence
another in stochastic processes, enabling efficient prediction of RNA secondary
structure including pseudoknots.