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RNA multiple structural alignment with longest common subsequences

Author

Listed:
  • Sergey Bereg

    (University of Texas at Dallas)

  • Marcin Kubica

    (Warsaw University)

  • Tomasz Waleń

    (Warsaw University)

  • Binhai Zhu

    (Montana State University)

Abstract

In this paper, we present a new model for RNA multiple sequence structural alignment based on the longest common subsequence. We consider both the off-line and on-line cases. For the off-line case, i.e., when the longest common subsequence is given as a linear graph with n vertices, we first present a polynomial O(n 2) time algorithm to compute its maximum nested loop. We then consider a slightly different problem—the Maximum Loop Chain problem and present an algorithm which runs in O(n 5) time. For the on-line case, i.e., given m RNA sequences of lengths n, compute the longest common subsequence of them such that this subsequence either induces a maximum nested loop or the maximum number of matches, we present efficient algorithms using dynamic programming when m is small.

Suggested Citation

  • Sergey Bereg & Marcin Kubica & Tomasz Waleń & Binhai Zhu, 2007. "RNA multiple structural alignment with longest common subsequences," Journal of Combinatorial Optimization, Springer, vol. 13(2), pages 179-188, February.
    • Handle: RePEc:spr:jcomop:v:13:y:2007:i:2:d:10.1007_s10878-006-9020-x
    DOI: 10.1007/s10878-006-9020-x
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