Fusion: Practice and Applications FPA 2692-4048 2770-0070 10.54216/FPA https://www.americaspg.com/journals/show/3228 2018 2018 Faculty of Computer Science and Information Technology, Universiti Tun Hussein Onn Malaysia, 86400, Malaysia Mubarak Mubarak School of Computer Sciences, Universiti Sains Malaysia, Penang, 11800, Malaysia Rosni Abdullah School of Computer Sciences, Universiti Sains Malaysia, Penang, 11800, Malaysia Mohd. Adib Hj. Omar School of Computer Science and Informatics, De Montfort University, The Gateway, Leicester LE1 9BH, UK Abdulghani Ali Ahmed Faculty of Computer Science and Information Technology, Universiti Tun Hussein Onn Malaysia, 86400, Malaysia Nurul Aswa Omar Faculty of Computer Science and Information Technology, Universiti Tun Hussein Onn Malaysia, 86400, Malaysia Salama A. Mostafa Four kinds of smaller molecules known as ribonucleotide bases-adenine (A), cytosine (C), guanine (G), and uracil (U) combine to form the linear molecule known as ribonucleic acid (RNA). Aligning multiple sequences is a fundamental task in bioinformatics. This paper studies the correlation of different objective functions applying to RNA multiple sequence alignment (MSA) fusion generated by the Harmony search-based method. Experiments are performed on the BRAliBase dataset containing different numbers of test groups. The correlation of the alignment score and the quality obtained is compared against coffee, sum-of-pairs (SP), weight sum-of-pairs (WSP), NorMD, and MstatX. The results indicate that COFFEE and SP objective functions achieved a correlation coefficient (R²) of 0.96 and 0.92, respectively, when compared to the reference alignments, demonstrating their effectiveness in producing high-quality alignments. In addition, the sum-of-pairs takes less time than the COFFEE objective function for the same number of iterations on the same RNA benchmark. 2025 2025 1 10 10.54216/FPA.170201 https://www.americaspg.com/articleinfo/3/show/3228