Fast Structural Alignment of RNAs by Optimizing the Adjoining Order of Profile-csHMMs

A novel RNA structural alignment method has been proposed based on profile-csHMMs. In principle, the profile-csHMM based approach can handle any kind of RNA secondary structures including pseudoknots, and it has been shown that the proposed approach can find highly accurate RNA alignments. In order to find the optimal alignment, the method employs the SCA algorithm that can be used for finding the optimal state sequence of profile-csHMMs. The computational complexity of the SCA algorithm is not fixed, and it depends on the so-called adjoining order that describes how we can trace-back the optimal state sequence in a given profile-csHMM. Therefore, for fast RNA structural alignments, it is important to find the adjoining order that has the minimum computational cost. In this paper, we propose an efficient algorithm that can systematically find the optimal adjoining order that minimizes the computational cost for finding the RNA alignments. Numerical experiments show that employing the proposed algorithm can make the alignment speed up to 3.6 times faster, without any degradation in the quality of the RNA alignments.