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

Nora M. Villanueva (), Marta Sestelo, Miguel M. Fonseca and Javier Roca-Pardiñas
Additional contact information
Nora M. Villanueva: Centro de Investigación en Nanomateriais e Biomedicina (CINBIO), Universidade de Vigo, 36310 Vigo, Spain
Marta Sestelo: CITMAga, 15782 Santiago de Compostela, Spain
Miguel M. Fonseca: Department of Biochemistry, Genetics and Immunology, 36310 Vigo, Spain
Javier Roca-Pardiñas: CITMAga, 15782 Santiago de Compostela, Spain

Mathematics, 2023, vol. 11, issue 10, 1-20

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.

Keywords: R package; nonparametric model; multiple change points; bootstrap techniques; DNA compositional analysis (search for similar items in EconPapers)
JEL-codes: C (search for similar items in EconPapers)
Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.mdpi.com/2227-7390/11/10/2299/pdf (application/pdf)
https://www.mdpi.com/2227-7390/11/10/2299/ (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:gam:jmathe:v:11:y:2023:i:10:p:2299-:d:1147358

Access Statistics for this article

Mathematics is currently edited by Ms. Emma He

More articles in Mathematics from MDPI
Bibliographic data for series maintained by MDPI Indexing Manager ().