Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree

  • Bjarne Knudsen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2812)


Many methods in bioinformatics rely on evolutionary relationships between protein, DNA, or RNA sequences. Alignment is a crucial first step in most analyses, since it yields information about which regions of the sequences are related to each other. Here, a new method for multiple parsimony alignment over a tree is presented. The novelty is that an affine gap cost is used rather than a simple linear gap cost. Affine gap costs have been used with great success for pairwise alignments and should prove useful in the multiple alignment scenario. The algorithmic challenge of using an affine gap cost in multiple alignment is the introduction of dependence between different columns in the alignment. The utility of the new method is illustrated by a number of protein sequences where increased alignment accuracy is obtained by using multiple sequences.


Multiple Alignment Rooted Tree Pairwise Alignment Optimal Alignment Ancestral Sequence 
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.


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  1. 1.
    Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970)CrossRefGoogle Scholar
  2. 2.
    Hirschberg, D.S.: A linear space algorithm for computing maximal common subsequences. Comm. Assoc. Comp. Mach. 18, 341–343 (1975)zbMATHMathSciNetGoogle Scholar
  3. 3.
    Myers, E.W., Miller, W.: Optimal alignments in linear space. Comput. Appl. Biosci. 4, 11–17 (1988)Google Scholar
  4. 4.
    Gotoh, O.: An improved algorithm for matching biological sequences. J. Mol. Biol. 162, 705–708 (1982)CrossRefGoogle Scholar
  5. 5.
    Durbin, R., Eddy, S., Krogh, A., Mitchison, G.: Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge (1998)zbMATHCrossRefGoogle Scholar
  6. 6.
    Sankoff, D., Cedergren, R.J.: Simultaneous comparison of three or more sequences related by a tree. In: Sankoff, D., Kruskal, J.B. (eds.) Time Warps, String Edits, and Macromolecules: the Theory and Practice of Sequence Comparison, pp. 253–264. Addison-Wesley, Reading (1983)Google Scholar
  7. 7.
    Carrillo, H., Lipmann, D.: The multiple sequence alignment problem in biology. SIAM J. Appl. Math. 48, 1073–1082 (1988)zbMATHCrossRefMathSciNetGoogle Scholar
  8. 8.
    Feng, D.F., Doolittle, R.F.: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25, 351–360 (1987)CrossRefGoogle Scholar
  9. 9.
    Hein, J.: A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol. Biol. Evol. 6, 649–668 (1989)Google Scholar
  10. 10.
    Thompson, J.D., Higgins, D.G., Gibson, T.J.: 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 (1994)CrossRefGoogle Scholar
  11. 11.
    Fitch, W.M.: Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20, 406–416 (1971)CrossRefGoogle Scholar
  12. 12.
    Aho, A.V., Sloane, N.J.A.: Some doubly exponential sequences. Fib. Quart. 11, 429–437 (1973)zbMATHMathSciNetGoogle Scholar
  13. 13.
    Mizuguchi, K., Deane, C.M., Blundell, T.L., Overington, J.P.: HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 7, 2469–2471 (1998)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Bjarne Knudsen
    • 1
  1. 1.Department of ZoologyUniversity of FloridaGainesvilleUSA

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