Adapting Machine Learning Technique for Periodicity Detection in Nucleosomal Locations in Sequences

DNA sequence is an important determinant of the positioning, stability, and activity of nucleosome, yet the molecular basis of these remains elusive. Positioned nucleosomes are believed to play an important role in transcriptional regulation and for the organization of chromatin in cell nuclei. After completing the genome project of many organisms, sequence mining received considerable and increasing attention. Many works devoted a lot of effort to detect the periodicity in DNA sequences, namely, the DNA segments that wrap the Histone protein. In this paper, we describe and apply a dynamic periodicity detection algorithm to discover periodicity in DNA sequences. Our algorithm is based on suffix tree as the underlying data structure. The proposed approach considers the periodicity of alternative substrings, in addition to considering dynamic window to detect the periodicity of certain instances of substrings. We demonstrate the applicability and effectiveness of the proposed approach by reporting test results on three data sets.