Detection of Tandem Repeats in DNA Sequences Based on Parametric Spectral Estimation

Abstract

Tandem repeats, which occur frequently in genomes, are related to gene regulatory functions and various diseases. In this paper, an efficient algorithm for tandem repeat detection is proposed. In our method, the spectrogram of a DNA sequence is analyzed based on the autoregressive model. Then, significant peaks in the spectrogram are selected, and the corresponding regions in the DNA sequence are analyzed to search for tandem repeats. Experiment results show that our method has a superior performance in comparison with other algorithms.

Dot2dot: accurate whole-genome tandem repeats discovery

“…Despite the vast literature on TRs discovery tools [see Lim et al (2013) for a recent survey], only few algorithms are usable in practice. In fact, most tools seem to be no longer available or no longer supported (Abajian, 1994; Krishnan and Tang, 2004; Kurtz et al , 2001; Parisi et al , 2003; Pokrzywa and Polanski, 2010; Sokol et al , 2007; Taneda, 2004; Wirawan et al , 2010; Zhou et al , 2009); some other is still available but no longer maintained [this is the case e.g. Wexler et al (2005)] that is distributed only in binary form and requires an obsolete version of the operating system).…”

“…Exhaustive search of TRs, instead, is unaffordable because of the exponential growth of the dictionary size as a function of the allowed motif length. The dual approach is that of ab-initio methods (Benson, 1999; Boeva et al , 2006; Girgis and Sheetlin, 2013; Kofler et al , 2007; Kolpakov et al , 2003; Krishnan and Tang, 2004; Kurtz et al , 2001; Pellegrini et al , 2010; Sokol et al , 2007; Wexler et al , 2005; Wirawan et al , 2010; Zhou et al , 2009) that do not require any pre-existing knowledge about the input sequence. Although more complex, this class of algorithms is the most studied and used in practice.…”

The relationship between periodic dinucleotides and the nucleosomal DNA deformation revealed by normal mode analysis

“…Furthermore, periodicity exists in many parts of a genome. For example, there are many tandem repeats in the human genome [19,20], and exons, the coding regions in genes, have the periodicity of 3 bps [21,22]. It would be interesting to study whether the periodic nucleotide in these regions also have collective motions or cooperativity.…”