An evolutionary space-time model with varying among-site dependencies

Molecular Biology and Evolution

Volumn 23, Issue 2, 2006, Pages 392-400

  Stern, Adi ^a   Pupko, Tal ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

Evolutionary models; Hidden Markov models; Site specific evolutionary rates

Indexed keywords

POTASSIUM CHANNEL; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BAY REGION BINDING SITE; CORRELATION ANALYSIS; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; PROTEOMICS; SEQUENCE ANALYSIS; THEORETICAL MODEL;

EVOLUTION, MOLECULAR; MARKOV CHAINS; MODELS, GENETIC; POTASSIUM CHANNELS; PROTEIN STRUCTURE, TERTIARY;

EID: 30744435826     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj044     Document Type: Article

References (35)

1. Akaike, H. 1974. A new look at the statistical model identification. IEEE Trans. Automatic Control 119:716-723.
2. Aloy, P., E. Querol, F. X. Aviles, and M. J. Sternberg. 2001. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol. 311:395-408.
3. Anisimova, M., J. P. Bielawski, and Z. Yang. 2001. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol. Biol. Evol. 18:1585-1592.
4. Berglund, A. C., B. Wallner, A. Elofsson, and D. A. Liberles. 2005. Tertiary windowing to detect positive diversifying selection. J. Mol. Evol. 60:499-504.
5. Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242.
6. Doyle, D. A., J. Morais Cabral, R. A. Pfuetzner, A. Kuo, J. M. Gulbis, S. L. Cohen, B. T. Chait, and R. MacKinnon. 1998. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280:69-77.
7. Durbin, R., S. E. Eddy, A. Krogh, and G. Mitchison. 1998. Biological sequence analysis. Cambridge University Press, Cambridge.
8. Fares, M. A., S. F. Elena, J. Ortiz, A. Moya, and E. Barrio. 2002. A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. J. Mol. Evol. 55:509-521.
9. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
10. _. 2001. Taking variation of evolutionary rates between sites into account in inferring phylogenies. J. Mol. Evol. 53:447-455.
11. Felsenstein, J., and G. A. Churchill. 1996. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13:93-104.
12. Gu, X., Y. X. Fu, and W. H. Li. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-557.
13. Jiang, Y., A. Lee, J. Chen, M. Cadene, B. T. Chait, and R. MacKinnon. 2002. The open pore conformation of potassium channels. Nature 417:523-526.
14. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
15. Lio, P., and N. Goldman. 1998. Models of molecular evolution and phylogeny. Genome Res. 8:1233-1244.
16. MacKinnon, R. 2003. Potassium channels. FEBS Lett. 555:62-65.
17. Mayrose, I., N. Friedman, and T. Pupko. 2005. A gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics Suppl 2: ii151-ii158.
18. Mayrose, I., D. Graur, N. Ben-Tal, and T. Pupko. 2004. Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol. Biol. Evol. 21:1781-1791.
19. Mayrose, I., A. Mitchell, and T. Pupko. 2005. Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. J. Mol. Evol. 60:345-353.
20. Miller, C. 2000. An overview of the potassium channel family. Genome Biol. 1:REVIEWS0004.
21. Nei, M., and S. Kumar. 2000. Molecular evolution and phylogeny. Oxford University Press, Oxford.
22. Pupko, T., R. E. Bell, I. Mayrose, F. Glaser, and N. Ben-Tal. 2002. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18(Suppl. 1):S71-S77.
23. Robinson, D. M., D. T. Jones, H. Kishino, N. Goldman, and J. L. Thorne. 2003. Protein evolution with dependence among codons due to tertiary structure. Mol. Biol. Evol. 20:1692-1704.
24. Rodrigue, N., N. Lartillot, D. Bryant, and H. Philippe. 2005. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene 347:207-217.
25. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
26. Siepel, A., and D. Haussler. 2004. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21:468-488.
27. Sullivan, J., D. Swofford, and G. Naylor. 1999. The effect of taxon sampling on estimating rate heterogeneity parameters of maximum-likelihood models. Mol. Biol. Evol. 16:1347-1356.
28. Suzuki, Y. 2004. Three-dimensional window analysis for detecting positive selection at structural regions of proteins. Mol. Biol. Evol. 21:2352-2359.
29. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in D. M. Hillis and B. K. Mable, eds. 2nd ed. Molecular systematics. Sinauer Associates, Sunderland, Mass.
30. Wang, Z. O., and D. D. Pollock. 2005. Context dependence and coevolution among amino acid residues in proteins. Methods Enzymol. 395:779-790.
31. Yang, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
32. _. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
33. _. 1995. A space-time process model for the evolution of DNA sequences. Genetics 139:993-1005.
34. _. 1996. Among-site variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11:367-372.
35. Yang, Z., and T. Wang. 1995. Mixed model analysis of DNA sequence evolution. Biometrics 51:552-561.