Analysis of Objective Functions for Ribonucleic Acid Multiple Sequence Alignment Fusion Based on Harmony Search Algorithm

Mubarak Saif ^1,*, Rosni Abdullah², Mohd. Adib Hj. Omar², Abdulghani Ali Ahmed³, Nurul Aswa Omar¹ , Salama A. Mostafa¹

¹Faculty of Computer Science and Information Technology, Universiti Tun Hussein Onn Malaysia, 86400, Malaysia

²School of Computer Sciences, Universiti Sains Malaysia, Penang, 11800, Malaysia

³School of Computer Science and Informatics, De Montfort University, The Gateway, Leicester LE1 9BH, UK

Emails: mubaraksm@uthm.edu.my; rosni@usm.my; adib@usm.my; aa.ahmed@dmu.ac.uk; nurulaswa@uthm.edu.my; salama@uthm.edu.my

Abstract

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.

Keywords: Objective function; Harmony search; Ribonucleic acid (RNA); Multiple sequence alignment (MSA)