A computational model for RNA multiple structural alignment

Authors:
Eugene Davydov;Serafim Batzoglou
Affiliations:
Department of Computer Science, Stanford University, Stanford, CA 94305, USA;Department of Computer Science, Stanford University, Stanford, CA 94305, USA
Venue:
Theoretical Computer Science
Year:
2006

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Abstract

This paper addresses the problem of aligning multiple sequences of noncoding RNA (ncRNA) 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(log^2S).