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seq2R: An R Package to Detect Change Points in DNA Sequences

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Listed:
  • Nora M. Villanueva

    (Centro de Investigación en Nanomateriais e Biomedicina (CINBIO), Universidade de Vigo, 36310 Vigo, Spain
    Department of Statistics and Operations Research, SIDOR Research Group, University of Vigo, 36310 Vigo, Spain
    These authors contributed equally to this work.)

  • Marta Sestelo

    (CITMAga, 15782 Santiago de Compostela, Spain
    Department of Statistics and Operations Research, SIDOR Research Group, University of Vigo, 36310 Vigo, Spain
    These authors contributed equally to this work.)

  • Miguel M. Fonseca

    (Department of Biochemistry, Genetics and Immunology, 36310 Vigo, Spain)

  • Javier Roca-Pardiñas

    (CITMAga, 15782 Santiago de Compostela, Spain
    Department of Statistics and Operations Research, SIDOR Research Group, University of Vigo, 36310 Vigo, Spain)

Abstract

Identifying the mutational processes that shape the nucleotide composition of the mitochondrial genome (mtDNA) is fundamental to better understand how these genomes evolve. Several methods have been proposed to analyze DNA sequence nucleotide composition and skewness, but most of them lack any measurement of statistical support or were not developed taking into account the specificities of mitochondrial genomes. A new methodology is presented, which is specifically developed for mtDNA to detect compositional changes or asymmetries (AT and CG skews) based on nonparametric regression models and their derivatives. The proposed method also includes the construction of confidence intervals, which are built using bootstrap techniques. This paper introduces an R package, known as seq2R, that implements the proposed methodology. Moreover, an illustration of the use of seq2R is provided using real data, specifically two publicly available complete mtDNAs: the human ( Homo sapiens ) sequence and a nematode ( Radopholus similis ) mitogenome sequence.

Suggested Citation

  • Nora M. Villanueva & Marta Sestelo & Miguel M. Fonseca & Javier Roca-Pardiñas, 2023. "seq2R: An R Package to Detect Change Points in DNA Sequences," Mathematics, MDPI, vol. 11(10), pages 1-20, May.
    • Handle: RePEc:gam:jmathe:v:11:y:2023:i:10:p:2299-:d:1147358
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    References listed on IDEAS

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