A Transition Probability Model for Amino Acid Substitutions from Blocks

Journal of Computational Biology

Volumn 10, Issue 6, 2003, Pages 997-1010

  Veerassamy, Shalini ^a   Smith, Andrew ^a   Tillier, Elisabeth R M ^a  

^a PRINCESS MARGARET HOSPITAL   (Canada)

Author keywords

Amino acid substitution; Blocks database; Empirical probability model

Indexed keywords

AMINO ACID; PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANALYTIC METHOD; ARTICLE; MATHEMATICAL ANALYSIS; MOLECULAR EVOLUTION; MOLECULAR MODEL; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN DATABASE;

AMINO ACID SUBSTITUTION; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; MODELS, GENETIC; PROBABILITY; PROTEINS;

EID: 0742286995     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652703322756195     Document Type: Article

References (24)

1. Adachi, J., and Hasegawa, M. 1996. Model of amino acid substitution in protein encoded by mitochondrial DNA. J. Mol. Evol. 42, 459-468.
2. Adachi, J., Wadell, P.J., Martin, W., and Hasegawa, M. 2000. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol. 50, 348-358.
3. Altschul, S.F. 1991. Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219, 555-565.
4. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, J.D. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
5. Arvestad, L., and Bruno, W.J. 1997. Estimation of reversible substitution matrices from multiple pairs of sequences. J. Mol. Evol. 45, 696-703.
6. Burden, R.L., and Faires, J.D. 1985. Numerical Analysis, PWS, Boston, MA.
7. Dayhoff, M.R., Schwartz, R., and Orcutt, B. 1978. A model of evolutionary change in protein. Atlas of Protein Sequences and Structure 5, 345-352.
8. Devauchelle, C., Grossmann, A., Hénaut, A., Holschneider, M., Monnerot, M., Risler, J.L., and Torrésani, B. 2002. Rate matrices for analyzing large families of protein sequences. J. Comp. Biol. 8, 381-399.
9. Efron, B. 1979. Bootstrap methods: Another look at the jackknife. Ann. Statist. 7, 1-26.
10. Felsenstein, J. 2002. Phylip (phylogeny inference package) version 3.6.3. Distributed by the author.
11. Golub, G.H., and Van Loan, C.F. 1983. Matrix Computation, p. 384, Johns Hopkins University Press.
12. Gonnet, G., Cohen, M., and Benner, S. 1992. Exhaustive matching of the entire protein sequence database. Science 256, 1443-1445.
13. Henikoff, S., and Henikoff, J. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915-10919.
14. Henikoff, S., Henikoff, J., and Pietrokovski, S. 1999. Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics 15(6), 471-479.
15. 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.
16. Jukes, T.H., and Cantor, C.R. 1969. Evolution of Protein Molecules, 21-132, Academic Press, New York.
17. Krause, A.J., Stoye, J., and Vingron, M. 2000. The SYSTERS protein sequence cluster set. Proc. Natl. Acad. Sci. USA 28, 270-272.
18. Mitchison, G.J. 1999. A probabilistic treatment of phylogeny and sequence alignment. J. Mol. Evol. 49, 11-22.
19. Muller, T., and Vingron, M. 2000. Modeling amino acid replacement. J. Comp. Biol. 7, 761-776.
20. Pearson, W.R., and Lipman, D.J. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444-2448.
21. 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. Nucl. Acids Res. 22, 4673-4680.
22. Thorne, J.L. 2001. Models of protein sequence evolution and their applications. Curr. Opin. Gen. Dev. 10, 602-605.
23. Whelan, S., and Goldman, N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach. J. Mol. Evol. 18, 691-699.
24. Yang, S., Nielsen, R., and Hasegawa, M. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15, 1600-1611.