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Sequence alignment is a fundamental concept in bioinformatics that helps in comparing biological sequences such as DNA, RNA, or proteins to identify regions of similarity, which may indicate functional, structural, or evolutionary relationships. The process relies on arranging sequences to maximize their level of similarity, either through pairwise alignment, which involves two sequences, or multiple sequence alignment, which involves three or more sequences. The main principle of pairwise sequence alignment is to compare two sequences by inserting gaps to optimize the number of matches and minimize mismatches. This is achieved using scoring systems that assign positive scores for matches, negative scores ____ ____ ________ __________ _____.
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