What is pairwise sequence alignment?

Pairwise sequence alignment is the comparison of two sequences (DNA, RNA, or protein) to identify regions of similarity that may indicate functional, structural, or evolutionary relationships. There are two types: global alignment (aligns entire sequences end-to-end, best for similar-length sequences with high similarity, uses Needleman-Wunsch algorithm) and local alignment (finds regions of high similarity within sequences, useful for sequences with different lengths or partial similarity, uses Smith-Waterman algorithm). Alignment scoring considers matches, mismatches, and gaps using scoring matrices like BLOSUM or PAM for proteins.