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International Conference on Parallel Computing in Fluid Dynamics

ParCFD 2013: Parallel Computational Fluid Dynamics pp 460–469Cite as

A Divide-and-Conquer Method for Multiple Sequence Alignment on Multi-core Computers

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Part of the book series: Communications in Computer and Information Science ((CCIS,volume 405))

Abstract

A parallel Divide-and-Conquer Alignment procedure (DCA) for multiple sequence alignment is presented. DCA improves alignment speed by using the Divide-and-Conquer paradigm, which is suitable for handling large-scale processing problems on multi-core computers. DCA works by dividing the large-scale alignment problem into smaller and more tractable sub-problems which can be solved by the existing algorithms. We assess the execution time and accuracy of our implementation of DCA on an 8-core computer using the classical benchmarks, BAliBASE, PREFAB, IRMBase and OXBENCH, and twenty-eight artificially generated test sets. DCA achieves up to 111-fold improvements in execution time with comparable accuracy.

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Author information

Authors and Affiliations

  1. School of Computer Science, Zhaoqing University, Zhaoqing, 526061, China

    Xiangyuan Zhu

Authors
  1. Xiangyuan Zhu
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Editor information

Editors and Affiliations

  1. College of Information Science and Engineering, Hunan University, 410082, Changsha, China

    Kenli Li

  2. College of Information Science and Engineering, Hunan University, #2, South Lushan Road, Yuelu District, 410082, Changsha, China

    Zheng Xiao  & Jiayi Du  & 

  3. College of Information Science and Engineering, Northeastern University, 110004, Shenyang, China

    Yan Wang

  4. Hunan University, State University of New York at New Paltz,, 12561, New Paltz, NY, USA

    Keqin Li

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© 2014 Springer-Verlag Berlin Heidelberg

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Zhu, X. (2014). A Divide-and-Conquer Method for Multiple Sequence Alignment on Multi-core Computers. In: Li, K., Xiao, Z., Wang, Y., Du, J., Li, K. (eds) Parallel Computational Fluid Dynamics. ParCFD 2013. Communications in Computer and Information Science, vol 405. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-53962-6_41

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  • DOI: https://doi.org/10.1007/978-3-642-53962-6_41

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-53961-9

  • Online ISBN: 978-3-642-53962-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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