A Computational Model for RNA Multiple Structural Alignment.

Abstract. 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).

• Type: Conference
• Year: 2004
• Where: CPM
• Authors: Eugene Davydov, Serafim Batzoglou
• Keywords: CPM 2004, Graph Theoretic Model, Non-coding Rna Genes, RNA Multiple Alignment