A Computational Model for RNA Multiple Structural Alignment

This paper addresses the problem of aligning multiple sequences of non-coding RNA genes. We approach this problem with the biologically motivated paradigm that scoring of ncRNA alignments should be based primarily on secondary structure rather than nucleotide conservation. We introduce a novel graph theoretic model (NLG) for analyzing algorithms based on this approach, prove that the RNA multiple alignment problem is NP-Complete in this model, and present a polynomial time algorithm that approximates the optimal structure of size S within a factor of O(log2 S).