Scoring Algorithm for Context-Sensitive HMMs with Application to RNA Secondary Structure Analysis

During the last decade, a number of evidences have been found that non-coding RNAs (ncRNA) are involved in various important processes. Many of these ncRNAs are known to conserve their secondary structure, which gives rise to complex dependencies between distant bases in the primary sequence. Therefore, we need more complex models than the traditional HMM in order to analyze ncRNAs. Recently, contextsensitive HMMs (csHMM) have been proposed for modeling RNA secondary structures. In this paper, we propose a dynamic programming algorithm that can be used for scoring csHMMs.