Global Alignment


Global alignment is a means of showing the similarities and differences of two or more sequences, compared along their entire length.

Keywords: Needleman–Wunsch algorithm; score; gap penalty; dynamic programming

Figure 1.

Spreadsheet representation of a dynamic programming matrix for the comparison of TACAGTC and TACAGC.



Carrilo H and Lipman D (1988) The multiple sequence alignment problem in biology. SIAM Journal on Applied Mathematics 48: 1073–1082.

Dayhoff M, Schwartz RM and Orcutt BC (1978) A model of evolutionary change in proteins. In: Dayhoff M (ed.) Atlas of Protein Sequence and Structure, supplement 3, pp. 345–352. Silver Spring, MD: National Biomedical Research Foundation.

Feng D and Doolittle R (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal of Molecular Evolution 25: 351–360.

Gupta SK, Kececioglu J and Schäffer AA (1995) Improving the practical space and time efficiency of the shortest‐paths approach to sum‐of‐pairs multiple sequence alignment. Journal of Computational Biology 2: 459–472.

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Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position‐specific gap penalties, and weight matrix choice. Nucleic Acids Research 22: 4673–4680.

Further Reading

Gusfield D (1997) Part III: inexact matching, sequence alignment, dynamic programming. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, pp. 209–392. New York, NY: Cambridge University Press.

Pevzner P (2001) Computational Molecular Biology: an Algorithmic Approach, chaps 6 and 7, pp. 93–132. Cambridge, MA: MIT Press.

Setubal JC and Meidanis J (1997) Sequence comparison and database search. Introduction to Computational Molecular Biology, chap. 3, pp. 47–104. Boston, MA: PWS Publishing.

Waterman MS (1995) Introduction to Computational Biology: Maps, Sequences, and Genomes, chaps 9 and 10, pp. 183–252. Cambridge, UK: Chapman & Hall.

Web Links

European Bioinformatics Institute (EBI). Global (and local) pairwise alignment web server

Institut de Génétique Humaine (IGH). Global pairwise alignment web server‐guess.cgi

Michigan State University (MTU). Pairwise alignment web server with several oprions

University of Southern California (USC). Pairwise alignment web server with several oprions www‐

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Meidanis, Joao(Sep 2005) Global Alignment. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0005256]