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Study of triplet periodicity differences inside and between genomes

Author

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  • Suvorova Yulia M.

    (Bioinformatics Laboratory, Centre of Bioengineering of the Russian Academy of Sciences, 117312, Prospect 60-tya Oktyabrya, Moscow, Russian Federation)

  • Korotkov Eugene V.

    (Bioinformatics Laboratory, Centre of Bioengineering of the Russian Academy of Sciences, 117312, Prospect 60-tya Oktyabrya, Moscow, Russian Federation Department of Applied Mathematics, National Nuclear Investigational University (MIFI), 115522, Kashirskoe Shosse, 31, Moscow, Russian Federation)

Abstract

Triplet periodicity (TP) is a distinctive feature of the protein coding sequences of both prokaryotic and eukaryotic genomes. In this work, we explored the TP difference inside and between 45 prokaryotic genomes. We constructed two hypotheses of TP distribution on a set of coding sequences and generated artificial datasets that correspond to the hypotheses. We found that TP is more similar inside a genome than between genomes and that TP distribution inside a real genome dataset corresponds to the hypothesis which implies that a common TP pattern exists for the majority of sequences inside a genome. Additionally, we performed gene classification based on TP matrixes. This classification showed that TP allows identification of the genome to which a given gene belongs with more than 85% accuracy.

Suggested Citation

  • Suvorova Yulia M. & Korotkov Eugene V., 2015. "Study of triplet periodicity differences inside and between genomes," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 14(2), pages 113-123, April.
    • Handle: RePEc:bpj:sagmbi:v:14:y:2015:i:2:p:113-123:n:1
    DOI: 10.1515/sagmb-2013-0063
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    References listed on IDEAS

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    1. José, Marco V. & Govezensky, Tzipe & Bobadilla, Juan R., 2005. "Statistical properties of DNA sequences revisited: the role of inverse bilateral symmetry in bacterial chromosomes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 351(2), pages 477-498.
    2. Jon Bohlin & Eystein Skjerve, 2009. "Examination of Genome Homogeneity in Prokaryotes Using Genomic Signatures," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-12, December.
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