Multiple Sequence Alignment Using Chemical Reaction Optimization Algorithm

  • Md. Shams Wadud
  • Md. Rafiqul Islam
  • Nittyananda KunduEmail author
  • Md. Rayhanul Kabir
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 941)


In bioinformatics, Multiple Sequence Alignment (MSA) is an NP-complete problem. This alignment problem is important in computational biology due to its usefulness in extracting and representing biological importance among sequences by finding similar regions. MSA is also helpful for finding the secondary or tertiary structure of the protein and using it critical anonymousness motives of DNA or Protein can also be found. For solving the problem, we have proposed a method based on Chemical Reaction Optimization (CRO). We have redesigned the basic four operators of CRO and three new operators have been designed to solve the problem. The additional operators are needed in order to arrange the base symbols properly. For testing the efficiency of our proposed method DNA sequences have taken from the different sources. We have compared the experimental results of the proposed method with clustal-omega and got better results for DNA sequences.


Multiple sequence alignment Meta-heuristic Chemical reaction optimization algorithm Sum of pair Repair mechanism 


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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Md. Shams Wadud
    • 1
  • Md. Rafiqul Islam
    • 1
  • Nittyananda Kundu
    • 1
    Email author
  • Md. Rayhanul Kabir
    • 1
  1. 1.Computer Science and Engineering DisciplineKhulna UniversityKhulnaBangladesh

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