Comparative analysis of periodicity search methods in DNA sequences

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. (C) 2014 Elsevier Ltd. All rights reserved.