Abstract
Sequence alignment is an important fundamental subject in bioinformatics research, which is an important measure to discover the function, structure and evolutionary information in biological sequences. At first, we use the maximum likelihood method for estimated the relevance parameters in this paper, while under the JC69 model and Markov models of biological genetic evolution for calculation the synonymous and non-synonymous substitutions rate and classified. So proposed to increase the calculated measure of the rate of biological evolution - K a and K s values of the calculated parameters of thought, that is improve the calculation of the parameters about synonymous and non-synonymous substitutions. Then according to K84 and HKY85 model parameter estimation analysis, we bring forward the new method of calculate the relevance parameters t and k in this paper. Finally, we select the appropriate gene sequence data, according to the two methods to calculate the synonymous and non-synonymous substitutions rate and the relevance parameters.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Yang, Z.: Mathematical Modeling. FuDan University Publishing Press, Beijing (August 2003)
Yang, Z.: Estimating Synonymous and Nonsynonymous Substitution Rates Under Realistic Evolutionary Models
He, S.: Probability Theory. Peking Univwesity Publishing Press, Beijing (2007)
Chen, J.: Statistics. High Education Publishing Press, Beijing (2009)
Merl, D., Escalante, A.: Comparison of Bayesian, maximum likelihood and parsimony methods for detecting positive selection (2008)
Zhang, Y.: Distributed Parallel Algorithm Designing, Analysis and Realization Doctor Thesis of Electronic Science and Technology University (2001)
Chen, Y.: Network Parallel BEM for Band Precision Rolling, Computational Mechanics. In: WCCM VI in Conjunction with APCOM 2004, Beijing, China, vol. 9, pp. 5–10. Tsinghua University Press/Springer (2004)
Psister, G.F.: Clusters of Computers: Characteristics of an Invisible Architecture. In: IEEE Int’l. Parallel Processing Symp. Honolulu (1996)
Saad, Y., Schultz, M.H.: GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetrical Linear System. SIAM J. Sci. Comp. 7(3), 856–869 (1986)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Jin, D., Niu, Z. (2010). Improvement of PAML Algorithm and Application. In: Zhu, R., Zhang, Y., Liu, B., Liu, C. (eds) Information Computing and Applications. ICICA 2010. Communications in Computer and Information Science, vol 106. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16339-5_48
Download citation
DOI: https://doi.org/10.1007/978-3-642-16339-5_48
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-16338-8
Online ISBN: 978-3-642-16339-5
eBook Packages: Computer ScienceComputer Science (R0)