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doi:10.1016/j.tcs.2006.09.013 
Copyright © 2006 Published by Elsevier B.V.
A computational model for RNA multiple structural alignment
Available online 29 September 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(log2S).
