Smith-Waterman Algorithm for Sequence Alignment
The Smith-Waterman algorithm is a dynamic programming algorithm used for sequence alignment of two biological sequences, such as DNA or protein sequences. It was developed by Temple Smith and Michael Waterman in 1981.
The algorithm works by calculating a matrix of scores for all possible pairs of positions in the two sequences. The scores are based on a scoring function that assigns a score to each possible match or mismatch of nucleotides or amino acids. The algorithm then identifies the optimal alignment by tracing back from the highest-scoring position in the matrix.
The Smith-Waterman algorithm is particularly useful for identifying local similarities between sequences, where only a portion of the sequences match, rather than global similarities, where the entire sequences match. It is widely used in bioinformatics for tasks such as sequence database searches, protein structure prediction, and phylogenetic analysis.
One limitation of the Smith-Waterman algorithm is its computational complexity, which makes it impractical for aligning very long sequences. However, there are many optimized versions of the algorithm that address this issue, such as the BLAST and FASTA algorithms