Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repea

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 fun...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Vladimir Paar, Nenad Pavin, Ivan Basar, Marija Rosandic, Matko Gluncic, Nils Paar
• Keywords: BMCBI 2008, Equidistant, Periodicity Peaks, Primary Periodicity Peaks