title: Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.
abstract: BACKGROUND
  Identification of approximate tandem repeats is an important task of broad significance and still remains a challenging problem of computational genomics. Often there is no single best approach to periodicity detection and a combination of different methods may improve the prediction accuracy. Discrete Fourier transform (DFT) has been extensively used to study primary periodicities in DNA sequences. Here we investigate the application of DFT method to identify and study alphoid higher order repeats.
  
  
  RESULTS
  We used method based on DFT with mapping of symbolic into numerical sequence to identify and study alphoid higher order repeats (HOR). For HORs the power spectrum shows equidistant frequency pattern, with characteristic two-level hierarchical organization as signature of HOR. Our case study was the 16 mer HOR tandem in AC017075.8 from human chromosome 7. Very long array of equidistant peaks at multiple frequencies (more than a thousand higher harmonics) is based on fundamental frequency of 16 mer HOR. Pronounced subset of equidistant peaks is based on multiples of the fundamental HOR frequency (multiplication factor n for nmer) and higher harmonics. In general, nmer HOR-pattern contains equidistant secondary periodicity peaks, having a pronounced subset of equidistant primary periodicity peaks. This hierarchical pattern as signature for HOR detection is robust with respect to monomer insertions and deletions, random sequence insertions etc. For a monomeric alphoid sequence only primary periodicity peaks are present. The 1/fbeta- noise and periodicity three pattern are missing from power spectra in alphoid regions, in accordance with expectations.
  
  
  CONCLUSIONS
  DFT provides a robust detection method for higher order periodicity. Easily recognizable HOR power spectrum is characterized by hierarchical two-level equidistant pattern: higher harmonics of the fundamental HOR-frequency (secondary periodicity) and a subset of pronounced peaks corresponding to constituent monomers (primary periodicity). The number of lower frequency peaks (secondary periodicity) below the frequency of the first primary periodicity peak reveals the size of nmer HOR, i.e., the number n of monomers contained in consensus HOR.
authors.affiliation: Faculty of Science, University of Zagreb, Bijenicka 32, Zagreb, Croatia. paar@hazu.hr
authors.forename: Vladimir
authors.initials: V
authors.lastname: Paar
authors.forename: Nenad
authors.initials: N
authors.lastname: Pavin
authors.forename: Ivan
authors.initials: I
authors.lastname: Basar
authors.forename: Marija
authors.initials: M
authors.lastname: Rosandić
authors.forename: Matko
authors.initials: M
authors.lastname: Gluncić
authors.forename: Nils
authors.initials: N
authors.lastname: Paar
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000235:genetics; D030561:Databases, Nucleic Acid; D005583:Fourier Analysis; D006801:Humans; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences
chemical_list: D004247:DNA