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Authors: N. Gadura ; Todd Holden ; G. Tremberger Jr ; E. Cheung ; P. Schneider ; D. Lieberman and T. Cheung

Affiliation: CUNY Queensborogh Community College, United States

ISBN: 978-989-674-019-1

Keyword(s): Mono-nucleotide entropy, Di-nucleotide entropy, Fractal dimension, Neanderthal mt-DNA COX2, Neanderthal mt-DNA 16S rRNA.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Sequence Analysis

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.

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Paper citation in several formats:
Gadura N.; Holden T.; Tremberger Jr G.; Cheung E.; Schneider P.; Lieberman D.; Cheung T. and (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

@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},
}

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

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