title: Comparative analysis of periodicity search methods in DNA sequences.
abstract: To determine the periodicity of a DNA sequence, different spectral approaches are applied (discrete Fourier transform (DFT), autocorrelation (CORR), information decomposition (ID), hybrid method (HYB), concept of spectral envelope for spectral analysis (SE), normalized autocorrelation (CORR_N) and profile analysis (PA). In this work, we investigated the possibility of finding the true period length, by depending on the average number of accumulated changes in DNA bases (PM) for the methods stated above. The results show that for periods with short length (≤4 b.p), it is possible to use the hybrid method (HYB), which combines properties of autocorrelation, Fourier transform, and information decomposition (ID). For larger period lengths (>4) with values of point mutation (PM) equal to 1.0 or more per one nucleotide, it is preferable to use information of decomposition method (ID), as the other spectral approaches cannot achieve correct determination of the period length present in the analyzed sequence.
authors.affiliation: Centre of Bioengineering Russian Academy of Sciences, Prospect 60-tya Oktyabrya 7/1, Moscow 117312, Russian Federation. Electronic address: suvorovay@gmail.com.
authors.forename: Yulia M
authors.initials: YM
authors.lastname: Suvorova
authors.affiliation: National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe Shosse, 31, Moscow 115522, Russian Federation. Electronic address: bioinf@rambler.ru.
authors.forename: Maria A
authors.initials: MA
authors.lastname: Korotkova
authors.affiliation: Centre of Bioengineering Russian Academy of Sciences, Prospect 60-tya Oktyabrya 7/1, Moscow 117312, Russian Federation; National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe Shosse, 31, Moscow 115522, Russian Federation. Electronic address: genekorotkov@gmail.com.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Korotkov
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D018509:DNA, Helminth / Q000235:genetics*; D005583:Fourier Analysis; D015233:Models, Statistical; D009711:Nucleotides; D010507:Periodicity; D017354:Point Mutation; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data*
chemical_list: D018509:DNA, Helminth; D009711:Nucleotides
keywords: DNA sequence analysis; Fourier analysis; correlation; information decomposition; periodicity