A Hybrid-Based Harmony Search Algorithm for RNA Multiple Sequence Alignment

摘要

Multiple sequence alignment (MSA) is an important topic in the field of computational molecular biology. Scalability, computational complexity as well as biological accuracy, are currently required for MSA methods. Finding an accurate alignment from primary sequences is computationally NP-hard problem. The aim of this study is to investigate and explore the capability of meta-heuristic technique known as harmony search algorithm (HS) to address MSA problem. This study introduces BHS-MSA, MHS-MSA, and HHS-MSA methods based on harmony search algorithm. Using a well-known benchmark (BRAliBase), the proposed method HHS-MSA showed better results compare to (BHS-MSA and MHS-MSA). HHS-MSA produced comparative results in terms of quality (Q) and total column (TC) and achieved good results in certain test groups especially alignments with large sequences.