Smith–Waterman Algorithm


The Smith–Waterman algorithm is a computer algorithm that finds regions of local similarity between DNA or protein sequences.

Keywords: DNA; protein; sequence alignment

Figure 1.

Local alignment of the DNA sequences TTACCGGCCAACTAA, ACCGTGTCACTAAC. Aligned portions are shown in upper case and unaligned portions of the sequences are shown in lower case.

Figure 2.

Global alignment for the example shown in Figure .

Figure 3.

Dot matrix for the optimal local alignment between sequences, showing cells in which the corresponding row and column letters match; cells lying on the optimal alignment that match; and where the path through the cell is a mismatch or gap.



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Further Reading

Waterman MS (1995) Introduction to Computational Biology Maps, Sequences and Genomes. Boca Raton, FL: CRC Press.

Web Links

Pfam (protein families database of alignments and HMMs). Updated May 2002

SMART (simple modular architecture research tool). Updated May 2002 http://smart.embl‐

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How to Cite close
Mott, Richard(Sep 2005) Smith–Waterman Algorithm. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0005263]