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RNA Tree Comparisons via Unrooted Unordered Alignments

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Algorithms in Bioinformatics (WABI 2012)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7534))

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Abstract

We generalize some current approaches for RNA tree alignment, which are traditionally confined to ordered rooted mappings, to also consider unordered unrooted mappings. We define the Homeomorphic Subtree Alignment problem, and present a new algorithm which applies to several modes, including global or local, ordered or unordered, and rooted or unrooted tree alignments. Our algorithm generalizes previous algorithms that either solved the problem in an asymmetric manner, or were restricted to the rooted and/or ordered cases. Focusing here on the most general unrooted unordered case, we show that our algorithm has an O(n T n S min (d T , d S )) time complexity, where n T and n S are the number of nodes and d T and d S are the maximum node degrees in the input trees T and S, respectively. This maintains (and slightly improves) the time complexity of previous, less general algorithms for the problem. Supplemental materials, source code, and web-interface for our tool are found in http://www.cs.bgu.ac.il/~negevcb/FRUUT .

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Author information

Authors and Affiliations

  1. Dept. of Computer Science, Ben-Gurion University of the Negev, Israel

    Nimrod Milo, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz & Michal Ziv-Ukelson

  2. Dept. of Computer Science and Engineering, UC San Diego, La Jolla, CA, USA

    Shay Zakov

Authors
  1. Nimrod Milo
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  2. Shay Zakov
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  3. Erez Katzenelson
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  4. Eitan Bachmat
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  5. Yefim Dinitz
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  6. Michal Ziv-Ukelson
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Editor information

Editors and Affiliations

  1. Department of Computer Science, Brown University, P.O. Box 1910, 02912, Providence, CA, USA

    Ben Raphael

  2. Department of Computer Science and Engineering, University of South Carolina, 301 Main Street, 29208, Columbia, SC, USA

    Jijun Tang

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© 2012 Springer-Verlag Berlin Heidelberg

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Milo, N., Zakov, S., Katzenelson, E., Bachmat, E., Dinitz, Y., Ziv-Ukelson, M. (2012). RNA Tree Comparisons via Unrooted Unordered Alignments. In: Raphael, B., Tang, J. (eds) Algorithms in Bioinformatics. WABI 2012. Lecture Notes in Computer Science(), vol 7534. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33122-0_11

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  • DOI: https://doi.org/10.1007/978-3-642-33122-0_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-33121-3

  • Online ISBN: 978-3-642-33122-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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