scoring matrices

Scoring matrices are tools used to evaluate how well two sequences—like strings of DNA, proteins, or words—align with each other. They assign numerical scores to pairs of elements (such as amino acids or letters), indicating how favorable or unfavorable their match is. For example, matching identical elements might get a high score, while mismatched or incompatible pairs get lower or negative scores. These matrices help algorithms determine the best possible alignment by summing the scores across the entire sequences, enabling scientists to identify similarities, differences, or functional relationships between biological molecules or data strings effectively.