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Pairwise Global Sequence Alignment Using Sine-Cosine Optimization Algorithm

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The International Conference on Advanced Machine Learning Technologies and Applications (AMLTA2018) (AMLTA 2018)

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 723))

Abstract

Pairwise global sequence alignment is a vital process for finding functional and evolutionary similarity between biological sequences. The main usage of it is searching biological databases for finding the origin of unknown sequence. The standard global alignment based on dynamic programming approach which produces the accurate alignment but with extensive execution time. In this paper, Sine-Cosine optimization algorithm was used for accelerating pairwise global alignment with alignment score near one produced by dynamic programming alignment. The reason for using Sine-Cosine optimization is its excellent exploration of the search space. The developed technique was tested on human and mouse protein sequences and its success for finding alignment similarity 75% of that produced by standard technique.

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Author information

Authors and Affiliations

  1. Computer and Systems Engineering Department, Faculty of Engineering, Zagazig University, Zagazig, Egypt

    Mohamed Issa, Ahmed Helmi & Ibrahim Ziedan

  2. Faculty of Computer and Information, Cairo University, Giza, Egypt

    Aboul Ella Hassanien

  3. Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt

    Ahmed Alzohairy

  4. Scientific Research Group in Egypt (SRGE), Cairo, Egypt

    Mohamed Issa & Aboul Ella Hassanien

Authors
  1. Mohamed Issa
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  2. Aboul Ella Hassanien
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  3. Ahmed Helmi
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  4. Ibrahim Ziedan
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  5. Ahmed Alzohairy
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Corresponding author

Correspondence to Mohamed Issa .

Editor information

Editors and Affiliations

  1. Faculty of Computers and Information, Information Technology Department, Cairo University, Giza, Egypt

    Aboul Ella Hassanien

  2. Faculty of Computers and Information Sciences, Ain Shams University, Cairo, Egypt

    Mohamed F. Tolba

  3. Faculty of Computers and Information, Department of Computer Science and Engineering, Mansoura University, Dakahlia, Egypt

    Mohamed Elhoseny

  4. Arab Academy for Science, Technology and Maritime Transport (AASTMT), Dokki, Egypt

    Mohamed Mostafa

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Issa, M., Hassanien, A.E., Helmi, A., Ziedan, I., Alzohairy, A. (2018). Pairwise Global Sequence Alignment Using Sine-Cosine Optimization Algorithm. In: Hassanien, A., Tolba, M., Elhoseny, M., Mostafa, M. (eds) The International Conference on Advanced Machine Learning Technologies and Applications (AMLTA2018). AMLTA 2018. Advances in Intelligent Systems and Computing, vol 723. Springer, Cham. https://doi.org/10.1007/978-3-319-74690-6_11

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  • DOI: https://doi.org/10.1007/978-3-319-74690-6_11

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-74689-0

  • Online ISBN: 978-3-319-74690-6

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