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SynPAM—A Distance Measure Based on Synonymous Codon Substitutions
October-December 2007 (vol. 4 no. 4)
pp. 553-560
ASCII Text
x 
 
Adrian Schneider, Gaston Gonnet, Gina Cannarozzi, "SynPAM—A Distance Measure Based on Synonymous Codon Substitutions," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. 4, pp. 553-560, October-December, 2007.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2007.1071,
author = {Adrian Schneider and Gaston Gonnet and Gina Cannarozzi},
title = {SynPAM—A Distance Measure Based on Synonymous Codon Substitutions},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {4},
number = {4},
issn = {1545-5963},
year = {2007},
pages = {553-560},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2007.1071},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - SynPAM—A Distance Measure Based on Synonymous Codon Substitutions
IS - 4
SN - 1545-5963
SP553
EP560
EPD - 553-560
A1 - Adrian Schneider,
A1 - Gaston Gonnet,
A1 - Gina Cannarozzi,
PY - 2007
KW - synonymous substitutions
KW - evolutionary distance
KW - SynPAM
KW - molecular evolution
KW - dS
VL - 4
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Measuring evolutionary distances between DNA or protein sequences forms the basis of many applications in computational biology and evolutionary studies. Of particular interest are distances based on synonymous substitutions, since these substitutions are considered to be under very little selection pressure and therefore assumed to accumulate in an almost clock-like manner. SynPAM, the method presented here, allows the estimation of distances between coding DNA sequences based on synonymous codon substitutions. The problem of estimating an accurate distance from the observed substitution pattern is solved by maximum-likelihood with empirical codon substitution matrices employed for the underlying Markov model. Comparisons with established measures of synonymous distance indicate that SynPAM has less variance and yields useful results over a longer time range.

[1] T. Miyata and T. Yasunaga, “Molecular Evolution of mRNA: A Method for Estimating Evolutionary Rates of Synonymous and Amino Acid Substitutions from Homologous Nucleotide Sequences and Its Application,” J. Molecular Evolution, vol. 16, pp.23-36, 1980.
[2] F. Perler, A. Efstratiadis, P. Lomedico, W. Gilbert, R. Kolodner, and J. Dodgson, “The Evolution of Genes: The Chicken Preproinsulin Gene,” Cell, vol. 20, no. 2, pp. 555-566, 1980.
[3] N. Goldman and Z. Yang, “A Codon-Based Model of Nucleotide Substitution for Protein-Coding DNA Sequences,” Molecular Biology and Evolution, vol. 11, no. 5, pp. 725-736, 1994.
[4] S.V. Muse, “Estimating Synonymous and Nonsynonymous Substitution Rates,” Molecular Biology and Evolution, vol. 13, no. 1, pp.105-114, 1996.
[5] Z. Yang, R. Nielsen, N. Goldman, and A.-M.K. Pedersen, “Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites,” Genetics, vol. 155, pp. 432-449, 2000.
[6] S.A. Benner, “Interpretive Proteomics—Finding Biological Meaning in Genome and Proteome Databases,” Advances in Enzyme Regulation, vol. 43, pp. 271-359, 2003.
[7] M.D. Caraco, “Neutral Evolutionary Distance: A New Dating Tool and Its Applications,” PhD dissertation, ETH Zürich, 2002.
[8] Z. Yang, “PAML: A Program Package for Phylogenetic Analysis by Maximum Likelihood,” Computer Applications in the Biosciences, vol. 13, pp. 555-556, 1997.
[9] Z. Yang and R. Nielsen, “Estimating Synonymous and Nonsynonymous Substitution Rates under Realistic Evolutionary Models,” Molecular Biology and Evolution, vol. 17, no. 1, pp. 32-43, 2000.
[10] A. Schneider, G.H. Gonnet, and G.M. Cannarozzi, “Synonymous Codon Substitution Matrix,” Proc. Sixth Int'l Conf. Computational Science (ICCS '06), V.N. Alexandrov, G.D. van Albada, P.M.A.Sloot, and J. Dongarra, eds., pp. 630-637, 2006.
[11] A. Schneider, G.M. Cannarozzi, and G.H. Gonnet, “Empirical Codon Substitution Matrix,” BMC Bioinformatics, vol. 6, no. 134, 2005.
[12] M.O. Dayhoff, R.M. Schwartz, and B.C. Orcutt, “A Model for Evolutionary Change in Proteins,” Atlas of Protein Sequence and Structure, M.O. Dayhoff, ed., vol. 5, pp. 345-352, Nat'l Biomedical Research Foundation, 1978.
[13] A. Siepel and D. Haussler, “Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood,” Molecular Biology and Evolution, vol. 21, no. 3, pp. 468-488, 2004.
[14] S.L. Kosakovsky Pond and S.V. Muse, “Site-to-Site Variation of Synonymous Substitution Rates,” Molecular Biology and Evolution, vol. 22, no. 12, pp. 2375-2385, 2005.
[15] D. Cox and H. Miller, The Theory of Stochastic Processes. Chapman and Hall, 1965.
[16] C. Dessimoz, G. Cannarozzi, M. Gil, D. Margadant, A. Roth, A. Schneider, and G. Gonnet, “OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements,” Proc. RECOMB Workshop Comparative Genomics (RCG '05), A. McLysath and D.H. Huson, eds., pp. 61-72, 2005.
[17] J.P. Bielawski, K.A. Dunn, and Z. Yang, “Rates of Nucleotide Substitution and Mammalian Nuclear Gene Evolution: Approximate and Maximum-Likelihood Methods Lead to Different Conclusions,” Genetics, vol. 156, pp. 1299-1308, 2000.
[18] K.A. Dunn, J.P. Bielawski, and Z. Yang, “Substitution Rates in Drosophila Nuclear Genes: Implications for Translational Selection,” Genetics, vol. 157, pp. 295-305, 2001.
[19] T.F. Smith and M.S. Waterman, “Identification of Common Molecular Subsequences,” J. Molecular Biology, vol. 147, pp. 195-197, 1981.
[20] O. Gotoh, “An Improved Algorithm for Matching Biological Sequences,” J. Molecular Biology, vol. 162, pp. 705-708, 1982.
[21] G.M. Cannarozzi, A. Schneider, and G.H. Gonnet, “A Phylogenomic Study of Dog, Mouse and Human,” PLoS Computational Biology, vol. 3, no. 1:e2, 2007.
[22] J.O. Kriegs, G. Churakov, M. Kiefmann, U. Jordan, J. Brosius, and J. Schmitz, “Retroposed Elements as Archives for the Evolutionary History of Placental Mammals,” PLoS Biology, vol. 4, no. 4, 2006.
[23] G.H. Gonnet, M.T. Hallett, C. Korostensky, and L. Bernardin, “Darwin v.2.0: An Interpreted Computer Language for the Biosciences,” Bioinformatics, vol. 16, no. 2, pp. 101-103, 2000.
[24] Y. Nakamura, T. Gojobori, and T. Ikemura, “Codon Usage Tabulated from the International DNA Sequence Database,” Nucleic Acids Research, vol. 28, p. 292, 2000.
[25] T. Kulikova, P. Aldebert, N. Althorpe, W. Baker, K. Bates, P. Browne, A. van den Broek, G. Cochrane, K. Duggan, R. Eberhardt, N. Faruque, M. Garcia-Pastor, N. Harte, C. Kanz, R. Leinonen, Q. Lin, V. Lombard, R. Lopez, R. Mancuso, M. McHale, F. Nardone, V. Silventoinen, P. Stoehr, G. Stoesser, M.A. Tuli, K. Tzouvara, R. Vaughan, D. Wu, W. Zhu, and R. Apweiler, “The EMBL Nucleotide Sequence Database,” Nucleic Acids Research, vol. 32, pp. D27-D30, 2004.
[26] T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X.M. Fernandez-Suarez, J. Gilbert, M. Hammond, J. Herrero, H. Hotz, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, F. Kokocinsci, D. London, I. Longden, G. McVicker, C. Melsopp, P. Meidl, S. Potter, G. Proctor, M. Rae, D. Rios, M. Schuster, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and E. Birney, “Ensembl 2005,” Nucleic Acids Research, vol. 33, supplement 1, pp. D447-D453, 2005.

Index Terms:
synonymous substitutions, evolutionary distance, SynPAM, molecular evolution, dS
Citation:
Adrian Schneider, Gaston Gonnet, Gina Cannarozzi, "SynPAM—A Distance Measure Based on Synonymous Codon Substitutions," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. 4, pp. 553-560, Oct.-Dec. 2007, doi:10.1109/TCBB.2007.1071
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