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Sequence Alignment Algorithms for Run-Length-Encoded Strings

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Computing and Combinatorics (COCOON 2008)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5092))

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Abstract

A unified framework is applied to solving various sequence comparison problems for run-length encoded strings. All of these algorithms take O( min {mn′,m′n}) time and O( max {m,n}) space, for two strings of lengths m and n, with m′ and n′ runs, respectively. We assume the linear-gap model and make no assumption on the scoring matrices, which maximizes the applicability of these algorithms. The trace (i.e., the way to align two strings) of an optimal solution can also be recovered within the same time and space bounds.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Information Engineering, National Chi Nan University, Taiwan

    Guan Shieng Huang & Yue Li Wang

  2. Department of Information Management, Shih Hsin University, Taiwan

    Jia Jie Liu

Authors
  1. Guan Shieng Huang
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  2. Jia Jie Liu
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  3. Yue Li Wang
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Xiaodong Hu Jie Wang

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© 2008 Springer-Verlag Berlin Heidelberg

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Huang, G.S., Liu, J.J., Wang, Y.L. (2008). Sequence Alignment Algorithms for Run-Length-Encoded Strings. In: Hu, X., Wang, J. (eds) Computing and Combinatorics. COCOON 2008. Lecture Notes in Computer Science, vol 5092. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69733-6_32

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  • DOI: https://doi.org/10.1007/978-3-540-69733-6_32

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-69732-9

  • Online ISBN: 978-3-540-69733-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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