Data compression and genomes: A two-dimensional life domain map

We define the complexity of DNA sequences as the information content per nucleotide, calculated by means of some Lempel–Ziv data compression algorithm. It is possible to use the statistics of the complexity values of the functional regions of different complete genomes to distinguish among genomes o...

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Bibliographic Details
Published in:Journal of theoretical biology Vol. 253; no. 2; pp. 281 - 288
Main Authors: Menconi, Giulia, Benci, Vieri, Buiatti, Marcello
Format: Journal Article
Language:English
Published: England Elsevier Ltd 21.07.2008
Subjects:
Algorithms
Animals
Archaea
Base Sequence
Data Compression - methods
DNA - genetics
DNA sequences
Evolution, Molecular
Evolutionary dynamics
Genome
Lempel–Ziv compression
Models, Genetic
Statistical analysis
Lempel–Ziv compression
Statistical analysis
Algorithms
DNA sequences
Evolutionary dynamics
ISSN:0022-5193, 1095-8541, 1095-8541
Online Access:Get full text
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Summary:We define the complexity of DNA sequences as the information content per nucleotide, calculated by means of some Lempel–Ziv data compression algorithm. It is possible to use the statistics of the complexity values of the functional regions of different complete genomes to distinguish among genomes of different domains of life (Archaea, Bacteria and Eukarya). We shall focus on the distribution function of the complexity of non-coding regions. We show that the three domains may be plotted in separate regions within the two-dimensional space where the axes are the skewness coefficient and the curtosis coefficient of the aforementioned distribution. Preliminary results on 15 genomes are introduced.
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ISSN:0022-5193
1095-8541
1095-8541
DOI:10.1016/j.jtbi.2008.03.011