Advertisement

The Clustal Series of Programs for Multiple Sequence Alignment

  • Julie D. Thompson
Protocol
  • 2.2k Downloads
Part of the Springer Protocols Handbooks book series (SPH)

Abstract

Sequence comparison or alignment is one of the fundamental tools in molecular biology. Alignments are used to search the sequence databases for homologous proteins, in the identification of conserved regions in a set of related sequences, for twodimensional (2-D)/3-D structure predictions, phylogenetic studies, and so on. The comparison of biological sequences began in the early seventies, with the first dynamic programming algorithm for the global (or full-length) alignment of two sequences (1). Dynamic programming is a rigorous mathematical technique that is guaranteed to find the maximal scoring alignment for any two sequences. The optimal local alignment between a pair of sequences, in which only the highest-scoring subsegments of the two sequences are aligned, involves a simple modification (2) to the Needleman-Wunsch method.

Keywords

Multiple Alignment Output File Dynamic Programming Algorithm Guide Tree Alignment Parameter 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Needleman, S. B. and Wunsch, C. D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453.PubMedCrossRefGoogle Scholar
  2. 2.
    Smith, T. F. and Waterman, M. S. (1981) The identification of common molecular subsequences. J. Mol. Biol. 147, 195–197.PubMedCrossRefGoogle Scholar
  3. 3.
    Sankoff, D. (1975) Minimal mutation trees of sequences. SIAM J. Appl. Math. 28, 35–42.CrossRefGoogle Scholar
  4. 4.
    Feng, D. F. and Dolittle, R. F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25, 351–360.PubMedCrossRefGoogle Scholar
  5. 5.
    Myers, E. W. and Miller, W. (1988) Optimal alignments in linear space. CABIOS 4, 11–17.PubMedGoogle Scholar
  6. 6.
    Higgins, D. G. and Sharp, P. M. (1988) CLUSTAL: a package for performing multiple sequence alignments on a microcomputer. Gene 73, 237–244.PubMedCrossRefGoogle Scholar
  7. 7.
    Higgins, D. G. and Sharp, P. P. (1989) Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS 5, 151–153.PubMedGoogle Scholar
  8. 8.
    Higgins, D. G., Bleasby, A. J., and Fuchs, R. (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci. 8, 189–191.PubMedGoogle Scholar
  9. 9.
    Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.PubMedGoogle Scholar
  10. 10.
    Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.CrossRefGoogle Scholar
  11. 11.
    Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.PubMedCrossRefGoogle Scholar
  12. 12.
    Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876–4882.PubMedCrossRefGoogle Scholar
  13. 13.
    Page, R. D. (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 4, 357–358.Google Scholar
  14. 14.
    Perrire, G. and Gouy, M. (1996) WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364–369.CrossRefGoogle Scholar
  15. 15.
    Gribskov, M., McLachlan, A. D., and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. USA 84, 4355–4358.PubMedCrossRefGoogle Scholar
  16. 16.
    Wilbur, W. J. and Lipman, D. J. (1983) Rapid similarity searches of nucleic acid and protein data banks. Proc. Natl. Acad. Sci. USA 80, 726–730.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2005

Authors and Affiliations

  • Julie D. Thompson
    • 1
  1. 1.Laboratorie de Biologie et Genomique StructuralesInstitut de Genetique et de Biologie Moleculaire et CellulaireFrance

Personalised recommendations