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Man-Machine Interactions 3 pp 173–181Cite as

Bit-Parallel Algorithm for the Block Variant of the Merged Longest Common Subsequence Problem

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Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 242))

Abstract

The problem of comparison of genomic sequences is of great importance. There are various measures of similarity of sequences. One of the most popular is the length of the longest common subsequence (LCS). We propose the first bit-parallel algorithm for the variant of the LCS problem, block merged LCS, which was recently formulated in the studies on the whole genome duplication hypothesis. Practical experiments show that our proposal is from 10 to over 100 times faster than existing algorithms.

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Author information

Authors and Affiliations

  1. Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland

    Agnieszka Danek & Sebastian Deorowicz

Authors
  1. Agnieszka Danek
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  2. Sebastian Deorowicz
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Corresponding author

Correspondence to Agnieszka Danek .

Editor information

Editors and Affiliations

  1. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Dr. Aleksandra Gruca

  2. Polish Academy of Sciences and Silesian University of Technology, Gliwice, Poland

    Tadeusz Czachórski

  3. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Stanisław Kozielski

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© 2014 Springer International Publishing Switzerland

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Danek, A., Deorowicz, S. (2014). Bit-Parallel Algorithm for the Block Variant of the Merged Longest Common Subsequence Problem. In: Gruca, D., Czachórski, T., Kozielski, S. (eds) Man-Machine Interactions 3. Advances in Intelligent Systems and Computing, vol 242. Springer, Cham. https://doi.org/10.1007/978-3-319-02309-0_18

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  • DOI: https://doi.org/10.1007/978-3-319-02309-0_18

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-02308-3

  • Online ISBN: 978-3-319-02309-0

  • eBook Packages: EngineeringEngineering (R0)

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