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 a factor-2 approximation which runs in O(n 2.5) 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.
This research is partially supported by EPSCOR Visiting Scholar’s Program and MSU Short-term Professional Development Program.
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Bereg, S., Zhu, B. (2005). RNA Multiple Structural Alignment with Longest Common Subsequences. In: Wang, L. (eds) Computing and Combinatorics. COCOON 2005. Lecture Notes in Computer Science, vol 3595. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11533719_6
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DOI: https://doi.org/10.1007/11533719_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28061-3
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