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A New Dynamic Programming Algorithm for Multiple Sequence Alignment

  • Conference paper
Combinatorial Optimization and Applications (COCOA 2007)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4616))

Abstract

Multiple sequence alignment (MSA) is one of the most basic and central tasks for many studies in modern biology. In this paper, we present a new progressive alignment algorithm for this very difficult problem. Given two groups A and B of aligned sequences, this algorithm uses Dynamic Programming and the sum-of-pairs objective function to determine an optimal alignment C of A and B. The proposed algorithm has a much lower time complexity compared with a previously published algorithm for the same task [11]. Its performance is extensively assessed on the well-known BAliBase benchmarks and compared with several state-of-the-art MSA tools.

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Author information

Authors and Affiliations

  1. LERIA - University of Angers, 2 bd Lavoisier, 49045 Angers Cedex 01, France

    Jean-Michel Richer, Vincent Derrien & Jin-Kao Hao

Authors
  1. Jean-Michel Richer
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  2. Vincent Derrien
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  3. Jin-Kao Hao
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Editor information

Andreas Dress Yinfeng Xu Binhai Zhu

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© 2007 Springer-Verlag Berlin Heidelberg

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Richer, JM., Derrien, V., Hao, JK. (2007). A New Dynamic Programming Algorithm for Multiple Sequence Alignment. In: Dress, A., Xu, Y., Zhu, B. (eds) Combinatorial Optimization and Applications. COCOA 2007. Lecture Notes in Computer Science, vol 4616. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73556-4_8

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  • DOI: https://doi.org/10.1007/978-3-540-73556-4_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-73555-7

  • Online ISBN: 978-3-540-73556-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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