SHANNON ENTROPY AND FRACTAL ANALYSIS FOR THE 16S RIBOSOMAL RNA AND COX2 MT-DNA SEQUENCES IN PRIMATES INCLUDING NEANDERTHAL

N. Gadura, Todd Holden, G. Tremberger Jr, E. Cheung, P. Schneider, D. Lieberman, T. Cheung

Abstract

The primate mt-DNA 16S rRNA and COX2 sequences, including Neanderthal sequences, were studied using nucleotide frequency, mono- and di-nucleotide entropy, and fractal dimension. The fractal dimension was computed with the Higuchi method when a nucleotide sequence is expressed as a numerical sequence where each nucleotide is assigned its proton number. The results shows that the C+G percent correlates with the fractal dimension with R-square value of around 0.88 (N = 8) for both gene sequences. The Di- and mono-nucleotide entropy is also well correlated with similar R-square values. For the COX2 gene, the human and Neanderthal cluster at high entropy suggests that chimp, gorilla, and orangutan were subjected to a higher selection pressure for this gene. The human COX2 has less entropy than the Neanderthal COX2 consistent with the presence of some selection pressure.

References

  1. Green, RE, 2008, Malaspinas AS, et al. “A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing”, Cell, 134, 416-426.
  2. Holden, T. 2008, G. Tremberger, Jr., P. Marchese, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, D. Lieberman, & T. Cheung, “DNA sequance based comparative studies of between nonextremophile and extremophile organisms with implications in exobiology”, SPIE Proceedings, 70970Q, (12 pages) invited.
  3. Higuchi, T., 1998, "Approach to an irregular time series on the basis of fractal theory", Physica D vol 31, 277- 283.
  4. Lee, Chang-Yong, 2006 “Mass Fractal Dimension of the Ribosome and Implication of its Dynamic Characteristics”, Physical Review E 73, 042901.
  5. Parkhomchuk, DV, 2006 ” Di-nucleotide Entropy as a Measure of Genomic Sequence Functionality”, arXiv:q-bio/0611059
  6. Pollard, KS 2006a, Salama SR, Lambert N, Coppens S, Pedersen JS, et al., “An RNA gene expressed during cortical development evolved rapidly in humans”. Nature 443, 167-172.
  7. Pollard KS, 2006b, Salama SR, King B, Kern AD, Dreszer T, et al. “Forces shaping the fastest evolving regions in the human genome”, PLoS Genet 2(10): e168. DOI: 10. 1371/journal.pgen.0020168
  8. Tremberger, Jr., George, E. Cheung; N. Gadura; T. Holden; R. Subramaniam; R. Sullivan; P. Schneider; A. Flamholz; D. Lieberman; T. Cheung, “Multi-fractal property of perchlorate reductase gene sequences and DNA photonics application to UV fluorescence detection on Mars-like surface”, SPIE Proceedings Vol. 7441, 74410G, (10 pages) invited, 2009
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Paper Citation


in Harvard Style

Gadura N., Holden T., Tremberger Jr G., Cheung E., Schneider P., Lieberman D. and Cheung T. (2010). SHANNON ENTROPY AND FRACTAL ANALYSIS FOR THE 16S RIBOSOMAL RNA AND COX2 MT-DNA SEQUENCES IN PRIMATES INCLUDING NEANDERTHAL . In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 257-260. DOI: 10.5220/0002753002570260


in Bibtex Style

@conference{bioinformatics10,
author={N. Gadura and Todd Holden and G. Tremberger Jr and E. Cheung and P. Schneider and D. Lieberman and T. Cheung},
title={SHANNON ENTROPY AND FRACTAL ANALYSIS FOR THE 16S RIBOSOMAL RNA AND COX2 MT-DNA SEQUENCES IN PRIMATES INCLUDING NEANDERTHAL},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={257-260},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002753002570260},
isbn={978-989-674-019-1},
}


in EndNote Style

TY - CONF
JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - SHANNON ENTROPY AND FRACTAL ANALYSIS FOR THE 16S RIBOSOMAL RNA AND COX2 MT-DNA SEQUENCES IN PRIMATES INCLUDING NEANDERTHAL
SN - 978-989-674-019-1
AU - Gadura N.
AU - Holden T.
AU - Tremberger Jr G.
AU - Cheung E.
AU - Schneider P.
AU - Lieberman D.
AU - Cheung T.
PY - 2010
SP - 257
EP - 260
DO - 10.5220/0002753002570260