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Fractal and Dynamical Language Methods to Construct Phylogenetic Tree Based on Protein Sequences from Complete Genomes

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Advances in Natural Computation (ICNC 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3612))

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Abstract

The complete genomes of living organisms have provided much information on their phylogenetic relationships. In the past few years, we proposed three alternative methods to model the noise background in the composition vector of protein sequences from a complete genome. The first method is based on the frequencies of the 20 kinds of amino acids appearing in the genome and the multiplicative model. The second method is based on the iterated function system model in fractal geometry. The last method is based on the relationship between a word and its two sub-words in the theory of symbolic dynamics. Here we introduce these methods. The complete genomes of prokaryotes and eukaryotes are selected to test these algorithms. Our distance-based phylogenetic tree of prokaryotes and eukaryotes agrees with the biologists’ “tree of life” based on the 16S-like rRNA genes in a majority of basic branches and most lower taxa.

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Author information

Authors and Affiliations

  1. Program in Statistics and Operations Research, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland, 4001, Australia

    Zu-Guo Yu & Vo Anh

  2. School of Mathematics and Computing Science, Xiangtan University, Hunan, 411105, China

    Zu-Guo Yu & Li-Quan Zhou

Authors
  1. Zu-Guo Yu
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  2. Vo Anh
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  3. Li-Quan Zhou
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Editors and Affiliations

  1. School of Electrical and Electronic Engineering, Nanyang Technological University, Block S1, Nanyang Avenue, 639798, Singapore

    Lipo Wang

  2. School of Software, Sun Yat-Sen University, 510275, Guangzhou, China

    Ke Chen

  3. School of Computer Engineering, Nanyang Technological University, BLK N4, 2b-39, Nanyang Avenue, 639798, Singapore

    Yew Soon Ong

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© 2005 Springer-Verlag Berlin Heidelberg

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Yu, ZG., Anh, V., Zhou, LQ. (2005). Fractal and Dynamical Language Methods to Construct Phylogenetic Tree Based on Protein Sequences from Complete Genomes. In: Wang, L., Chen, K., Ong, Y.S. (eds) Advances in Natural Computation. ICNC 2005. Lecture Notes in Computer Science, vol 3612. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11539902_40

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  • DOI: https://doi.org/10.1007/11539902_40

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28320-1

  • Online ISBN: 978-3-540-31863-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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