<![CDATA[Sequence alignment is fundamental in bioinformatics, with Smith-Waterman (local) and Needleman-Wunsch (global) algorithms widely applied. However, comparative analyses on highly similar viral genomes such as SARS-CoV-2 remain scarce. This study systematically evaluated both algorithms using the first 5,000 nucleotides of two SARS-CoV-2 genomes (29,903 and 29,684 nt) under four parameter configurations: standard, low gap penalty, high gap penalty, and high match reward. Performance was assessed through alignment score, sequence identity, gap distribution, execution time, and parameter sensitivity. Both algorithms produced identical sequence identity (97.80%), with 4,943 matches out of 5,054 positions. Smith-Waterman consistently yielded higher alignment scores (12.6-112 points advantage), while Needleman-Wunsch was substantially faster (0.7752 vs 3.9014 s), showing 5.03 times greater computational efficiency. These findings indicate that both methods are reliable for highly similar viral sequences, with a trade-off between scoring precision and computational speed. This study provides the first parameter-sensitive comparison for full SARS-CoV02 genomes, emphasizing how parameter tuning can influence performance outcomes. A key limitation is that the analysis was restricted to the first 5,000 nucleotides, which may not capture variability across the complete genome.]]>
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