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.

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

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.

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

The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012 .exe) is its ability to identify a broad variety of repeats of unbounded length that can be arbitrarily distant in sequences as large as human chromosomes. The efficacy is due to the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram. In this way, we obtain very fast, efficient and highly automatized repeat finding tool. The method is robust to substitutions and insertions/deletions, as well as to various complexities of the sequence pattern. We present several case studies of GRM use, in order to illustrate its capabilities: identification of a-satellite tandem repeats and higher order repeats (HORs), identification of Alu dispersed repeats and of Alu tandems, identification of Period 3 pattern in exons, implementation of ‘magnifying glass’ effect, identification of complex HOR pattern, identification of inter-tandem transitional dispersed repeat sequences and identification of long segmental duplications. GRM algorithm is convenient for use, in particular, in cases of large repeat units, of highly mutated and/ or complex repeats, and of global repeat maps for large genomic sequences (chromosomes and genomes).

Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

The identification and analysis of repetitive patterns are active areas of biological and computational research. Tandem repeats in telomeres play a role in cancer and hypervariable trinucleotide tandem repeats are linked to over a dozen major neurodegenerative genetic disorders. In this paper, we present an algorithm to identify the exact and inexact repeat patterns in DNA sequences based on orthogonal exactly periodic subspace decomposition technique. Using the new measure our algorithm resolves the problems like whether the repeat pattern is of period P or its multiple (i.e., 2P, 3P, etc.), and several other problems that were present in previous signal-processing-based algorithms. We present an efficient algorithm of O(NLw log Lw), where N is the length of DNA sequence and Lw is the window length, for identifying repeats. The algorithm operates in two stages. In the first stage, each nucleotide is analyzed separately for periodicity, and in the second stage, the periodic information of each nucleotide is combined together to identify the tandem repeats. Datasets having exact and inexact repeats were taken up for the experimental purpose. The experimental result shows the effectiveness of the approach.

/pdf/a-novel-signal-processing-measure-to-identify-exact-and-30rthe8kx3.pdf

A novel signal processing measure to identify exact and inexact tandem repeat patterns in DNA sequences

Finding repetitive sequences in DNA is of particular interest in biology due to their role in genetic diseases, human gene mapping, evolution, and many other important and interesting applications. We propose a method for finding hidden periodicities in DNA based on Fourier analysis. It is shown that this approach is effective for finding new repeat patterns that were previously undetected by some of the most popular algorithms published in the literature

A fourier product method for detecting approximate TANDEM repeats in DNA

The detection of tandem repeats is important in biology and medicine as it can be used for phylogenetic studies and disease diagnosis. The paper proposes two techniques for detecting approximate tandem repeats (ATRs) in DNA sequences. First, an evolutionary force heuristic is proposed to merge interspersed perfect tandem repeat sequences into an ATR structure. Next., a more general method is presented using a product spectrum of Fourier nucleotide subsequences to detect hidden periodicity. The Fourier method is sensitive to ATRs and is robust in the presence of substitutions, insertions, and deletions.

T.T. Tran

Papers

Techniques for detecting approximate tandem repeats in DNA