Amino acid-based phylogeny and alignment

Advances in Protein Chemistry

Volumn 54, Issue , 2000, Pages 99-135

  Higgins, Desmond G ^a  

^a UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; GENE DUPLICATION; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; REVIEW; SEQUENCE HOMOLOGY;

EID: 0033910362     PISSN: 00653233     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Review

References (44)

1. Adachi, J., and Hasegawa, M. (1992). MOLPHY: Programs for molecular phylogenetics, I. PROTML: maximum likelihood inference of protein phylogeny, Computer Science Monograph no. 27. Institute of Statistical Mathematics, Tokyo.
2. Altschul, S. F., Madden, T. L., Schaeffer, A. A., Zhang, J., Zhang, A., Miller, W., and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3398-3402.
3. Barton, G. J., and Sternberg, M. J. E. (1987). A strategy for the rapid multiple alignment of protein sequences. J. Mol. Biol. 198, 327-337.
4. Benian G. M., Kiff, J. E., Neckelmann, N., Moerman, D. G., and Waterston, R. H. (1989). Sequence of an unusually large protein implicated in regulation of myosin activity in C. elegans. Nature 342, 45-50.
5. Bork, P., and Dolittle, R. F. (1992). Proposed acquisition of an animal protein domain by bacteria. Proc. Natl. Acad. Sci. U.S.A. 89, 8990-8994.
6. Corpet, F. (1988). Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16, 10881-10890.
7. Dayhoff, M. O., Schwartz, R. M., and Orcutt, B. C. (1978). In "Atlas of Protein Sequence and Structure." (Dayhoff, M. O., ed.), NBRF, Washington, vol. 5, supplement 3, p. 345.
8. Felsenstein, J. (1985a). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
9. Felsenstein, J. (1985b). Confidence limits on phylogenies with a molecular clock. Syst. Zool. 34, 152-161.
10. Felsenstein, J. (1989). Phylip: phylogeny inference package (version 3.2). Cladistics 5, 164-166.
11. Felsenstein, J. (1996). Inferring phylogenies from protein sequences by parsimony, distance and Likelihood methods. In "Computer Methods for Macromolecular Sequence Analysis" (Doolittle, R. F., ed.), Methods Enzymol. 266, 418-427.
12. Feng, D.-F., and Doolittle, R. F. (1987). Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25, 351-360.
13. Fitch, W. M., and Margoliash, E. (1967). Construction of phylogenetic trees. Science 155, 279-284.
14. Galtier, N., Gouy, M., and Gautier, C. (1996). SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comp. Appl. Biosci. 12, 543-548.
15. Gibson, T. J., Rice, P. M., Thompson, J. D., and Heringa, J. (1993). KH domains within the FMR1 sequence suggest that Fragile-X syndrome stems from a defect in RNA metabolism. Trends Biochem. Sci. 18, 331-333.
16. Gotoh, O. (1982). An improved algorithm for matching biological sequences. J. Mol. Biol. 162, 705-708.
17. Gotoh, O. (1996). Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol. 264, 823-838.
18. Graur, D., and Higgins, D. G. (1994). Molecular evidence for the inclusion of cetaceans within the order artiodactyla. Mol. Biol. Evol. 11, 357-364.
19. Hegyi, H., and Bork, P. (1997). On the classification and evolution of protein modules. J. Protein Chem 16, 545-551.
20. Hein, J. (1989). A tree reconstruction 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.
21. Henikoff, S., and Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89, 10915-10919.
22. Higgins, D. G., and Sharp, P. M. (1988). CLUSTAL: a package for performing multiple sequence alignments on a microcomputer. Gene 73, 237-244.
23. Higgins, D. G., Thompson, J. D., and Gibson, T. J. (1996). Using CLUSTAL for multiple sequence alignment. In "Computer Methods for Macromolecular Sequence Analysis" (Doolittle, R. F., ed.), Methods Enzymol. 266, 383-402.
24. Jones, D. T., Taylor, W. R., and Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282.
25. Kimura, M. (1983). "The Neutral Theory of Molecular Evolution." Cambridge University Press, Cambridge, UK.
26. Li, W.-H., and Gouy, M. (1990). Statistical tests of molecular phylogenies. In "Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences." (Doolittle, R. F., ed.) Methods Enzymol. 183, 645-659.
27. Lipman, D. J., Altschul, S. F., and Kececioglu, J. D. (1989). A tool for multiple sequence alignment. Proc. Natl. Acad. Sci. U.S.A. 86, 4412-4415.
28. Livingstone, C. D., and Barton, G. J. (1993). Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci. 9, 745-756.
29. Maddison, W. P, and Maddison, D. R. (1989). Interactive analysis of phylogeny and character evolution using the computer program MacClade. Folia Primatol. 53, 190-202.
30. Musacchio, A., Gibson, T., Lehto, V. P., and Saraste, M. (1992). SH3 - An abundant protein domain in search of a function. FEBS Lett. 307, 55-61.
31. Needleman, S. B., and Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 48, 443-453.
32. Notredame, C., and Higgins, D. G. (1996). SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res. 24, 1515-1524.
33. Page, R. D. M. (1996). TREEVIEW: An application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12, 357-358.
34. Pearson W. R., and Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85, 2444-2448.
35. Saitou, N., and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
36. Smith, T. F., and Waterman, M. S. (1981). Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
37. Sneath, P. H. A., and Sokal, R. R. (1973). "Numerical Taxonomy."W. H. Freeman, San Francisco.
38. Sokal, R. R., and Michener, C. D. (1958). A statistical method for evaluating systematic relationships. University of Kansas Scientific Bulletin 28, 1409-1438.
39. Strimmer K., and von Haeseler, A. (1996). Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964-969.
40. Taylor, W. R. (1988). A flexible method to align large numbers of biological sequences. J. Mol. Evol. 28, 161-169.
41. 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.
42. 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.
43. Thompson, J. D., Plewniak, F., and Poch, O. (1999). BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 15, 87-88.
44. Zuckerkandl, E., and Pauling, L. (1965). Evolutionary divergence and convergence in proteins. In "Evolving Genes and Proteins" (V. Bryson and H. J. Vogel, eds.), pp. 97-166. Academic Press, New York.