Sequence utilities / Pairwise alignment
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Global alignment (Needleman–Wunsch) aligns two sequences end to end and suits sequences of similar length that are homologous throughout; local alignment (Smith–Waterman) finds the highest-scoring similar segment, useful for domains or short regions within long sequences.
In the text output “|” marks identical positions, “:” positive-scoring (similar) substitutions, “.” mismatches and a space a gap; numbers at the start and end of each line give positions in the original sequences.
Identity = identical positions ÷ alignment length (gaps included). Scores depend on the matrix and gap penalties and are comparable only under the same settings. The defaults (EDNAFULL for nucleotides, BLOSUM62 for proteins, gap opening 10, extension 0.5) match common alignment tools.
A gap of length L costs opening + (L − 1) × extension; end gaps are penalised too.
Needleman & Wunsch 1970 (J Mol Biol 48:443); Smith & Waterman 1981 (J Mol Biol 147:195); affine gaps, Gotoh 1982 (J Mol Biol 162:705); BLOSUM62, Henikoff & Henikoff 1992 (PNAS 89:10915). Scores match Biopython PairwiseAligner.
Up to 10,000 nt/aa per sequence.
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