A Hybrid Approach to Solve Multiple Sequence Alignment Problems Using Chaotic Metaheuristics

Aligning multiple sequences of amino acids or nucleotides is considered a challenging task in biology, like fitting puzzle pieces together to find the best matches. Due to the huge computational overhead of checking all possible combinations, simple metaheuristic approaches, such as genetic algorithms (GAs) that are inspired by nature, are good because they can effectively optimize the gap positions to get better scores. This work addresses this problem by combining GAs with chaotic sequences to obtain a better diversity in the search space that leads to near-optimal alignment. Chaotic sequences are known for their unpredictable patterns but structured behavior, which helps explore different solutions effectively. Integrating chaos theory into metaheuristics helps in achieving effective and accurate alignments of multiple sequences by handling complexity, finding optimal alignment, and improving efficiency. Users can adjust hyperparameters such as mutation probability, crossover probability, etc., making the approach flexible. The experiments are carried out on various inputs that are obtained from the BAliBASE dataset to establish the effectiveness and the superiority of the proposed approach. The proposed approach is compared with the state-of-the-art approaches, and the obtained outcomes are promising enough and encouraging to apply the proposed approach to real-life problems. Received: 26 March 2025 | Revised: 22 January 2026 | Accepted: 30 January 2026 Conflicts of Interest The authors declare that they have no conflicts of interest to this work. Data Availability Statement This article does not involve the creation or analysis of new data; therefore, the matter of data sharing does not apply to this study. The well-known BAliBASE dataset (https://www.lbgi.fr/balibase/) is used. Author Contribution Statement Gargi Nandi: Conceptualization, Methodology, Software, Investigation, Data curation, Writing – original draft, Visualization. Sweta Roy: Conceptualization, Methodology, Investigation, Data curation, Writing - original draft, Visualization. Yeasmin Khatun: Conceptualization, Methodology, Investigation, Data curation, Writing – original draft, Visualization. Nibedita Chakraborty: Validation, Formal analysis, Resources. Shrestha Pal: Validation, Formal analysis, Resources. Meheria Sultana Khatun: Validation, Formal analysis, Resources. Shouvik Chakraborty: Conceptualization, Methodology, Software, Investigation, Data curation, Writing – original draft, Writing – review & editing, Supervision, Project administration.