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Evidence of codon usage in the nearest neighbor spacing distribution of bases in bacterial genomes

Author

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  • Higareda, M.F.
  • Geiger, O.
  • Mendoza, L.
  • Méndez-Sánchez, R.A.

Abstract

Statistical analysis of whole genomic sequences usually assumes a homogeneous nucleotide density throughout the genome, an assumption that has been proved incorrect for several organisms since the nucleotide density is only locally homogeneous. To avoid giving a single numerical value to this variable property, we propose the use of spectral statistics, which characterizes the density of nucleotides as a function of its position in the genome. We show that the cumulative density of bases in bacterial genomes can be separated into an average (or secular) plus a fluctuating part. Bacterial genomes can be divided into two groups according to the qualitative description of their secular part: linear and piecewise linear. These two groups of genomes show different properties when their nucleotide spacing distribution is studied. In order to analyze genomes having a variable nucleotide density, statistically, the use of unfolding is necessary, i.e., to get a separation between the secular part and the fluctuations. The unfolding allows an adequate comparison with the statistical properties of other genomes. With this methodology, four genomes were analyzed Burkholderia, Bacillus, Clostridium and Corynebacterium. Interestingly, the nearest neighbor spacing distributions or detrended distance distributions are very similar for species within the same genus but they are very different for species from different genera. This difference can be attributed to the difference in the codon usage.

Suggested Citation

  • Higareda, M.F. & Geiger, O. & Mendoza, L. & Méndez-Sánchez, R.A., 2012. "Evidence of codon usage in the nearest neighbor spacing distribution of bases in bacterial genomes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(4), pages 1255-1269.
    • Handle: RePEc:eee:phsmap:v:391:y:2012:i:4:p:1255-1269
    DOI: 10.1016/j.physa.2011.10.035
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    References listed on IDEAS

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    1. Jan Vegelius & Svante Janson & Folke Johansson, 1986. "Measures of similarity between distributions," Quality & Quantity: International Journal of Methodology, Springer, vol. 20(4), pages 437-441, December.
    2. José, Marco V. & Govezensky, Tzipe & Bobadilla, Juan R., 2005. "Statistical properties of DNA sequences revisited: the role of inverse bilateral symmetry in bacterial chromosomes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 351(2), pages 477-498.
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