Optimizing Multiple Sequence Alignment: A Harris Hawks Optimization and Profile Alignment Hybrid Approach

Multiple Sequence Alignment (MSA) lines up three or more DNA or protein strings so we can see where they match. Laying those strings in neat, top-to-bottom rows is the backbone of jobs like spotting conserved motifs, tracing evolutionary branches, predicting how a protein will fold, and drafting PCR primers. In this study, we revisit the alignment task with a fresh recipe: the Harris Hawks Optimization (HHO) algorithm paired with a profile-alignment boost. HHO already has a solid record of cracking tough optimization puzzles, and the added profile layer sharpens its eye for biologically sensible matches. We aim to lift two trusted gauges of alignment quality, the Sum-of-Pairs (SP) and Column Score (CS) as high as they can go. By letting the hawks' search tactics work hand-in-hand with profile information, our hybrid delivers tighter fits. Tests on the BAliBASE 3.0 benchmark put this method head-to-head with leading MSA tools, and it repeatedly comes out on top, racking up the best SP and CS numbers. The upshot: this approach offers a strong new option for anyone chasing more precise sequence alignments across the life-sciences toolkit.