A Computational Model for RNA Multiple Structural Alignment

  • Eugene Davydov
  • Serafim Batzoglou
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3109)

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(log2S).

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Eugene Davydov
    • 1
  • Serafim Batzoglou
    • 1
  1. 1.Dept. of Computer ScienceStanford UniversityStanfordUSA

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