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Network clustering coefficient approach to DNA sequence analysis

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  • Gerhardt, Günther J.L.
  • Lemke, Ney
  • Corso, Gilberto

Abstract

In this work we propose an alternative DNA sequence analysis tool based on graph theoretical concepts. The methodology investigates the path topology of an organism genome through a triplet network. In this network, triplets in DNA sequence are vertices and two vertices are connected if they occur juxtaposed on the genome. We characterize this network topology by measuring the clustering coefficient. We test our methodology against two main bias: the guanine–cytosine (GC) content and 3-bp (base pairs) periodicity of DNA sequence. We perform the test constructing random networks with variable GC content and imposed 3-bp periodicity. A test group of some organisms is constructed and we investigate the methodology in the light of the constructed random networks. We conclude that the clustering coefficient is a valuable tool since it gives information that is not trivially contained in 3-bp periodicity neither in the variable GC content.

Suggested Citation

  • Gerhardt, Günther J.L. & Lemke, Ney & Corso, Gilberto, 2006. "Network clustering coefficient approach to DNA sequence analysis," Chaos, Solitons & Fractals, Elsevier, vol. 28(4), pages 1037-1045.
    • Handle: RePEc:eee:chsofr:v:28:y:2006:i:4:p:1037-1045
    DOI: 10.1016/j.chaos.2005.08.138
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    1. Oiwa, Nestor N & Glazier, James A, 2002. "The fractal structure of the mitochondrial genomes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 311(1), pages 221-230.
    2. Farkas, I. & Jeong, H. & Vicsek, T. & Barabási, A.-L. & Oltvai, Z.N., 2003. "The topology of the transcription regulatory network in the yeast, Saccharomyces cerevisiae," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 318(3), pages 601-612.
    3. H. Jeong & B. Tombor & R. Albert & Z. N. Oltvai & A.-L. Barabási, 2000. "The large-scale organization of metabolic networks," Nature, Nature, vol. 407(6804), pages 651-654, October.
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    Cited by:

    1. Xu, Na & Shang, Pengjian & Kamae, Santi, 2009. "Minimizing the effect of exponential trends in detrended fluctuation analysis," Chaos, Solitons & Fractals, Elsevier, vol. 41(1), pages 311-316.

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