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Simulated Annealing with Injecting Star-Alignment for Multiple Sequence Alignments

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Computational Intelligence and Security (CIS 2005)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 3801))

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Abstract

We present a novel algorithm SASAlignSimulated annealing with star-alignment. In the SASAlign, instead of starting with an initial solution chosen at random, we use the results formed by star-alignment to give a good starting point as the initial solution to the SA for further refinement. The time required by the algorithm scales linearly with the number of sequences in S, linearly with the number of iterations, and cube with the length of the sequences, that is O(Nnl 3). Experiments on the BAliBASE benchmark database also show that the proposed algorithm is efficient, and prove to be competitive with and better than the other method HMMT.

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Author information

Authors and Affiliations

  1. School of Computer Science and Technology, Xidian University, Xi’an, 710071, China

    Hongwei Huo & Hua Ming

Authors
  1. Hongwei Huo
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  2. Hua Ming
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Editor information

Editors and Affiliations

  1. Microelectronic Instiute, Xidian University, 710071, Xi’an, China

    Yue Hao

  2. Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong

    Jiming Liu

  3. School of Computer Science and Technology, Xidian University, Xi’an, China

    Yuping Wang

  4. Department of Computer Science, Hong Kong Baptist University, Hong Kong,  

    Yiu-ming Cheung

  5. School of Electrical and Electronic Engineering, University of Manchester, UK

    Hujun Yin

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

    Licheng Jiao

  7. Key Laboratory of Computer Networks and Information Security (Ministry of Education), Xidian University, 710071, Xi’an, China

    Jianfeng Ma

  8. National Laboratory of Antennas and Microwave Technology, Xidian University, 710071, Xi’an, Shanxi, P.R. China

    Yong-Chang Jiao

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© 2005 Springer-Verlag Berlin Heidelberg

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Huo, H., Ming, H. (2005). Simulated Annealing with Injecting Star-Alignment for Multiple Sequence Alignments. In: Hao, Y., et al. Computational Intelligence and Security. CIS 2005. Lecture Notes in Computer Science(), vol 3801. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11596448_121

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  • DOI: https://doi.org/10.1007/11596448_121

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-30818-8

  • Online ISBN: 978-3-540-31599-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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