Techniques for detecting approximate tandem repeats in DNA

Tran, Thao; Emanuele, Vincent A.; Zhou, Guolin

doi:10.1109/icassp.2004.1327144

Cited by 15 publications

(7 citation statements)

References 15 publications

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“…Fourier transform of a nucleotide sequence was represented also by sum of pure sequences (Eq. 3) or by their product [ 15 , 109 ]. A single binary sequence was used by mapping genomic sequence into purine/pyrimidine representation [ 22 ], or into weak bond/strong bond representation [ 109 ].…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2008

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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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Section: Methodsmentioning

confidence: 99%

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

et al. 2008

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“…In this paper, we have presented a novel SP-based approach for identifying exact and inexact tandem repeats in DNA sequences. In past, several algorithms and measures based on heuristic, combinatorial, dynamic programming, and SP approaches [5][6][7][8][9][10][11][12][13] have been proposed for finding tandem repeat structure in DNA sequences. SP-based algorithms for identifying tandem repeats have their own advantages because of its sensitivity towards detection of inexact repeats and application of faster signal processing tool like DFT.…”

Section: Introductionmentioning

confidence: 99%

“…Previous SP solutions to repeat pattern identification problem include the application of discrete Fourier transform (DFT) [11,12] and the application of short-time periodicity transform (STPT) [13]. In [11], DFT is used as a preprocessing tool for identifying the significant periodic regions through a sliding window analysis, and then an exact search method is used for finding the repetitive units.…”

Section: Introductionmentioning

confidence: 99%

A Novel Signal Processing Measure to Identify Exact and Inexact Tandem Repeat Patterns in DNA Sequences

Sarthi¹,

Mittal²,

Singh³

2007

EURASIP Journal on Bioinformatics and Systems Biology

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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 or its multiple (i.e., 2, 3, etc.), and several other problems that were present in previous signal-processing-based algorithms. We present an efficient algorithm of , where is the length of DNA sequence and 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.

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“…Aiming to overcome these limitations, scientists tried to find effective approach based on the signal processing techniques without prior information on targeted sequence. These approaches mainly use periodicity to detect STRs [26]. In this sense, the spectral analysis based on the exact periodic subspace decomposition and the autoregressive model (AR) were carried out [27].…”

Section: Introductionmentioning

confidence: 99%

Microsatellite’s Detection using the S -Transform Analysis based on the Synthetic and Experimental Coding

Zribi¹,

Messaoudi²,

Oueslati³

et al. 2019

ijacsa

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Microsatellite in genomic DNA sequence, or Short tandem repeat (STR). It is a class of tandem repeat that have repeated pattern with size of 2-6 base-pairs adjacent to each other. The detection of the specific tandem repeat is an important part of genetic diseases identification and it is also used in DNA fingerprinting and in evolutionary studies. Many tools based on string matching have been developed to detect microsatellites. However, these tools are based on prior information about repetitions in the sequence which cannot be always obtainable. For this, the signal processing techniques were suggested to overcome the limitations of the bioinformatic tools. In this paper, we use a new variant of the S-Transform which we apply to short tandem repeats signals. These signals are firstly obtained by applying different coding techniques to the DNA sequences. To further study the performance of the proposed method, we establish a comparison with different bioinformatics approaches (TRF, Mreps, Etandem) and three other methods of signal processing: The Adaptive S-Transform (AST), the Empirical Mode and Wavelet Decomposition (EMWD) and the Parametric Spectral Estimation (PSE) considering the AR model. This study indicates that our approach outperforms the earlier methods in identifying the short tandem repeat, in fact, our method detects the exact number and positions of trinucleotides present in the tested real DNA sequence.

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Techniques for detecting approximate tandem repeats in DNA

Cited by 15 publications

References 15 publications

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

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

A Novel Signal Processing Measure to Identify Exact and Inexact Tandem Repeat Patterns in DNA Sequences

Microsatellite’s Detection using the S -Transform Analysis based on the Synthetic and Experimental Coding

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