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

DOI10.1016/J.JTBI.2008.03.011MaRDI QIDQ1795081zbMATH OpenOpenAlexWikidataFDO

Authors Giulia Menconi, Vieri Benci, Marcello Buiatti

Publication date 16 October 2018

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0803.0465

zbMATH Keywords

algorithmsDNA sequencesevolutionary dynamicsLempel-Ziv compressionstatistical analysis

Mathematics Subject Classification ID

Coding and information theory (compaction, compression, models of communication, encoding schemes, etc.) (aspects in computer science) (68P30) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10)

Abstract: 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 noncoding 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.

Recommendations

• Sublinear growth of information in DNA sequences
• Correlations in DNA sequences across the three domains of life
• Similarity analysis of DNA sequences based on the generalized LZ complexity of (0,1)-sequences
• Multifractal characterisation of length sequences of coding and noncoding segments in a complete genome
• ANALYSIS OF THE EVOLVING PROTEOMES: PREDICTIONS OF THE NUMBER OF PROTEIN DOMAINS IN NATURE AND THE NUMBER OF GENES IN EUKARYOTIC ORGANISMS

Cites work

• A universal algorithm for sequential data compression
• Compression of individual sequences via variable-rate coding
• Computational information for the logistic map at the chaos threshold
• Dynamical systems and computable information
• scientific article; zbMATH DE number 3140804 (Why is no real title available?)
• scientific article; zbMATH DE number 3143967 (Why is no real title available?)
• scientific article; zbMATH DE number 1010621 (Why is no real title available?)
• In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: How to derive a coherent picture from global and local entropy measures
• Information and dynamical systems: A concrete measurement on sporadic dynamics
• The biological meanings of DNA correlations
• The multiple codes of nucleotide sequences
• Towards a statistical characterisation of the living state of matter

Cited in

(3)

• Sublinear growth of information in DNA sequences
• ANALYSIS OF THE EVOLVING PROTEOMES: PREDICTIONS OF THE NUMBER OF PROTEIN DOMAINS IN NATURE AND THE NUMBER OF GENES IN EUKARYOTIC ORGANISMS
• Computational Methods in Systems Biology

Describes a project that uses

Uses Software

• STAR

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