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DNA Compression Challenge Revisited: A Dynamic Programming Approach

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Combinatorial Pattern Matching (CPM 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3537))

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Abstract

Standard compression algorithms are not able to compress DNA sequences. Recently, new algorithms have been introduced specifically for this purpose, often using detection of long approximate repeats. In this paper, we present another algorithm, DNAPack, based on dynamic programming. In comparison with former existing programs, it compresses DNA slightly better, while the cost of dynamic programming is almost negligible.

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Author information

Authors and Affiliations

  1. LIX, Ecole Polytechnique, Palaiseau cedex, 91128, France

    Behshad Behzadi & Fabrice Le Fessant

Authors
  1. Behshad Behzadi
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  2. Fabrice Le Fessant
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Editor information

Editors and Affiliations

  1. Georgia Institute of Technology and Università di Padova,  

    Alberto Apostolico

  2. Université Paris-Est, France

    Maxime Crochemore

  3. School of Computer Science and Engineering, Seoul National University, 151-742, Seoul, Korea

    Kunsoo Park

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© 2005 Springer-Verlag Berlin Heidelberg

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Behzadi, B., Le Fessant, F. (2005). DNA Compression Challenge Revisited: A Dynamic Programming Approach. In: Apostolico, A., Crochemore, M., Park, K. (eds) Combinatorial Pattern Matching. CPM 2005. Lecture Notes in Computer Science, vol 3537. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11496656_17

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  • DOI: https://doi.org/10.1007/11496656_17

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-26201-5

  • Online ISBN: 978-3-540-31562-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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