Archaeon and archaeal virus diversity classification via sequence entropy and fractal dimension

George Tremberger Jr.; Victor Gallardo; Carola Espinoza; Todd Holden; N. Gadura; E. Cheung; P. Schneider; D. Lieberman; T. Cheung

doi:10.1117/12.860097

7 September 2010 Archaeon and archaeal virus diversity classification via sequence entropy and fractal dimension

George Tremberger Jr., Victor Gallardo, Carola Espinoza, Todd Holden, N. Gadura, E. Cheung, P. Schneider, D. Lieberman, T. Cheung

Author Affiliations +

Proceedings Volume 7819, Instruments, Methods, and Missions for Astrobiology XIII; 78190T (2010) https://doi.org/10.1117/12.860097
Event: SPIE Optical Engineering + Applications, 2010, San Diego, California, United States

Abstract

Archaea are important potential candidates in astrobiology as their metabolism includes solar, inorganic and organic energy sources. Archaeal viruses would also be expected to be present in a sustainable archaeal exobiological community. Genetic sequence Shannon entropy and fractal dimension can be used to establish a two-dimensional measure for classification and phylogenetic study of these organisms. A sequence fractal dimension can be calculated from a numerical series consisting of the atomic numbers of each nucleotide. Archaeal 16S and 23S ribosomal RNA sequences were studied. Outliers in the 16S rRNA fractal dimension and entropy plot were found to be halophilic archaea. Positive correlation (R-square ~ 0.75, N = 18) was observed between fractal dimension and entropy across the studied species. The 16S ribosomal RNA sequence entropy correlates with the 23S ribosomal RNA sequence entropy across species with R-square 0.93, N = 18. Entropy values correspond positively with branch lengths of a published phylogeny. The studied archaeal virus sequences have high fractal dimensions of 2.02 or more. A comparison of selected extremophile sequences with archaeal sequences from the Humboldt Marine Ecosystem database (Wood-Hull Oceanography Institute, MIT) suggests the presence of continuous sequence expression as inferred from distributions of entropy and fractal dimension, consistent with the diversity expected in an exobiological archaeal community.

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George Tremberger Jr., Victor Gallardo, Carola Espinoza, Todd Holden, N. Gadura, E. Cheung, P. Schneider, D. Lieberman, and T. Cheung "Archaeon and archaeal virus diversity classification via sequence entropy and fractal dimension", Proc. SPIE 7819, Instruments, Methods, and Missions for Astrobiology XIII, 78190T (7 September 2010); https://doi.org/10.1117/12.860097

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