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Hybrid genetic algorithms for the determination of DNA motifs to satisfy postulate 2-Optimality

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Abstract

Currently, determining DNA motifs or consensus plays an indispensable role in bioinformatics. Many postulates have been proposed for finding a consensus. Postulate 2-Optimality is essential for this task. A consensus satisfying postulate 2-Optimality is the best representative of a profile, and its distances to the profile members are uniform. However, this postulate has not been widely investigated in identifying a DNA motif or consensus for a DNA motif profile. The HDC algorithm is the best at this task in the literature. This study focuses on determining DNA motifs that satisfy postulate 2-Optimality. We propose a new hybrid genetic (HG1) algorithm based on the elitism strategy and local search. Subsequently, a novel elitism strategy and longest distance strategy are introduced to maintain the balance of exploration and exploitation. A new hybrid genetic (HG2) algorithm is developed based on the proposed exploration and exploitation balance approach. The simulation results show that these algorithms provide a high-quality DNA motif. The HG2 algorithm provides a DNA motif with the best quality.

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Authors and Affiliations

  1. Vietnam - Korea University of Information and Communication Technology, The University of Danang, Danang, Vietnam

    Dai Tho Dang

  2. Department of Applied Informatics, Faculty of Information and Communication Technology, Wrocław University of Science and Technology, Wrocław, Poland

    Ngoc Thanh Nguyen

  3. Faculty of Information Technology, Nguyen Tat Thanh University, Nguyen Tat Thanh, Vietnam

    Ngoc Thanh Nguyen

  4. Department of Computer Engineering, Yeungnam University, Yeungnam, Republic of Korea

    Dosam Hwang

Authors
  1. Dai Tho Dang
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  2. Ngoc Thanh Nguyen
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  3. Dosam Hwang
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Correspondence to Ngoc Thanh Nguyen or Dosam Hwang.

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This article belongs to the Topical Collection: Emerging Topics in Artificial Intelligence Selected from IEA/AIE2021 Guest Editors: Ali Selamat and Jerry Chun-Wei Lin

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Dang, D.T., Nguyen, N.T. & Hwang, D. Hybrid genetic algorithms for the determination of DNA motifs to satisfy postulate 2-Optimality. Appl Intell 53, 8644–8653 (2023). https://doi.org/10.1007/s10489-022-03491-7

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