Summary
This paper presents an essentially new method to construct phylogenetic trees from related amino acid sequences. The method is based on a new distance measure which describes sequence relationships by means of typical steric and physicochemical properties of the amino acids and is advantageous in some essential points. In particular, it avoids negative branches. The method was applied to different sets of protein sequences and the results compared with other well-established methods.
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References
BORK, P., and GRUNWALD, C. (1989): A method for property pattern searches in protein sequence databases, demonstrated by detection of GTP binding sites. Stud, biophys., 129, 231–240.
BORK, P., and GRUNWALD, C. (1990): Recognition of different nucleotide-binding sites in primary structures using a property pattern approach. Eur. J. Biochem., 191, 347–358.
FENG, D.-F., and DOOLITTLE, R. F. (1987): Progressive Sequence Alignment as Prerequisite to Correct Phylogenetic Trees. J. Mol. Evol., 25, 351–360.
FITCH, W. M., MARGOLIASH, E. (1967): Construction of phylogenetic trees. Science, 15, 279–284.
KLOTZ, L. C., BLANKEN, R. L. (1981): A practical method for calculating evolutionary trees from sequence data. J. Theor. Biol., 91, 261–272.
HARTMANIS, J., and STEARNS, R. E. (1966): Algebraic Structure Theory of Sequential Machines. Prentice-Hall, Englewood Cliffs. N.J.
MOORE, G. M., et al. (1973): An iterative approach from the standpoint of the additive hypothesis to the dendrogram problem posed by molecular data sets. J. Theor. Biol., 38, 423–457.
SANKOFF, D., et al. (1982): A strategy for sequence phylogeny research. Nucleic Acids Res., 10, 421–431.
TAYLOR, W. R. (1986): Identification of Protein Sequence Homology by Consensus Template Alignment. J. Mol. Biol., 188, 233–258.
PENNY, D., and HENDY, M. (1986): Estimating the reliability of evolutionary trees. Mol. Biol. Evol., 3, 403–411.
ZVELEBIL, M. J., et al. (1987): Prediction of Protein Secondary Structure and Active Sites using the Alignment of Homologous Sequences. J. Mol. Biol., 195, 957–961.
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© 1994 Springer-Verlag Berlin · Heidelberg
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Schmidt, W. (1994). Multiple Alignment of Protein Sequences and Construction of Evolutionary Trees based on Amino Acid Properties — an Algebraic Approach. In: Bock, HH., Lenski, W., Richter, M.M. (eds) Information Systems and Data Analysis. Studies in Classification, Data Analysis, and Knowledge Organization. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-46808-7_34
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DOI: https://doi.org/10.1007/978-3-642-46808-7_34
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-58057-7
Online ISBN: 978-3-642-46808-7
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