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Parallel Computing for Optimal Genomic Sequence Alignment

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Book cover Fuzzy Systems and Knowledge Discovery (FSKD 2006)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 4223))

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Abstract

This paper presents a new parallel algorithm, called “block-based wavefront”, to produce optimal pairwise alignment for biological sequences with reliable output and reasonable cost. It takes advantage of dynamic programming and parallel computing to produce optimal results in reasonable time. More importantly, the algorithm makes it possible for biologists to analyze datasets that were previously considered too long, often leading to memory overflow or prohibitively long time for computation.

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References

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Author information

Authors and Affiliations

  1. Faculty of Information Engineering, Shenzhen University, Shenzhen, 518060, China

    Zhihua Du & Zhen ji

  2. School of computer engineering, Nanyang Technological University, Singapore

    Zhihua Du & Feng Lin

Authors
  1. Zhihua Du
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  2. Zhen ji
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  3. Feng Lin
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Editor information

Editors and Affiliations

  1. School of Electrical and Electronic Engineering, Nanyang Technological University,, Block S1, Nanyang Avenue, 639798, Singapore

    Lipo Wang

  2. Life Science Research Center, School of Electronic Engineering, Xidian University,, 710071, Xi’an, Shaanxi, China

    Licheng Jiao

  3. School of Electrical and Electronic Engineering, Xidian University, 710071, Xi’an, China

    Guanming Shi

  4. School of Information Technology and Electrical Engineering, The University of Queensland, 4072, Brisbane, Queensland, Australia

    Xue Li

  5. College of Mathematics and Information Science, Hebei Normal University, 050016, Shijiazhuang, Hebei, P.R. China

    Jing Liu

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© 2006 Springer-Verlag Berlin Heidelberg

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Du, Z., ji, Z., Lin, F. (2006). Parallel Computing for Optimal Genomic Sequence Alignment. In: Wang, L., Jiao, L., Shi, G., Li, X., Liu, J. (eds) Fuzzy Systems and Knowledge Discovery. FSKD 2006. Lecture Notes in Computer Science(), vol 4223. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11881599_61

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  • DOI: https://doi.org/10.1007/11881599_61

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-45916-3

  • Online ISBN: 978-3-540-45917-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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