local alignment

Local alignment is a method used in bioinformatics to find regions of similarity between two sequences of nucleotides or amino acids. It involves identifying the best matching substrings (subsequences) within the two sequences, even if some parts of the sequences do not match at all. This is in contrast to global alignment, which tries to align the entire length of both sequences.

The local alignment algorithm uses a scoring system to assign a score to each possible alignment of two substrings. The algorithm then finds the highest scoring alignment and reports it as the best local alignment. This method is useful for identifying conserved regions in proteins or DNA sequences that may have undergone mutation or insertion/deletion events.