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).
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© 2004 Springer-Verlag Berlin Heidelberg
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Davydov, E., Batzoglou, S. (2004). A Computational Model for RNA Multiple Structural Alignment. In: Sahinalp, S.C., Muthukrishnan, S., Dogrusoz, U. (eds) Combinatorial Pattern Matching. CPM 2004. Lecture Notes in Computer Science, vol 3109. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-27801-6_19
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DOI: https://doi.org/10.1007/978-3-540-27801-6_19
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