Needleman–Wunsch algorithm

The Needleman–Wunsch algorithm uses dynamic programming to find an optimal global alignment between two sequences, maximizing a score defined by match, mismatch, and gap penalties.

Dynamic programming: A method that solves problems by combining solutions to overlapping subproblems. The algorithm fills a score matrix by reusing optimal alignments of shorter sequence prefixes.
Smith–Waterman algorithm: A dynamic-programming algorithm that finds the highest-scoring local alignment between sequences. Unlike Needleman–Wunsch, it permits alignment to start and end within the sequences.
Protein sequence alignment: The comparison of amino-acid sequences by arranging residues into corresponding positions. Substitution matrices let global alignment account for conservative and radical amino-acid changes.
Saul B. Needleman: An American biochemist who co-developed a dynamic-programming method for global biological sequence alignment. His collaboration gave the algorithm its first name.
Sequence alignment: The arrangement of biological sequences to identify corresponding positions and possible evolutionary or functional relationships. Needleman–Wunsch is a method for aligning sequences across their full lengths.
BLAST: A heuristic program for finding high-scoring local sequence similarities in large databases. BLAST trades guaranteed optimality for speed on database searches, unlike exact global alignment.
DNA sequence alignment: The arrangement of DNA nucleotide sequences to identify corresponding positions and differences. A simple match–mismatch score can make the algorithm useful for short DNA comparisons.
Christian D. Wunsch: An American biochemist who co-developed a dynamic-programming method for global biological sequence alignment. His collaboration with Needleman established the algorithm in sequence analysis.
Scoring matrix: A table assigning scores to pairs of symbols, such as amino acids or nucleotides. Substitution scores determine the value of matching or mismatching symbols in each matrix cell.
Local alignment: An alignment of the most similar subsequences, which may exclude unmatched sequence ends. It answers whether sequences share a strong region rather than how their entire lengths align.

Linked from 1 page