Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.
TLDR
DFT provides a robust detection method for higher order periodicity and is robust with respect to monomer insertions and deletions, random sequence insertions etc.Abstract:
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.read more
Citations
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Data Mining Techniques for the Life Sciences
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Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm
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Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription.
TL;DR: The comparison with available experimental data indicates that promoters with the most pronounced periodicities may be related to the supercoiling-sensitive genes.
References
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3-, 10.5-, 200- and 400-base periodicities in genome sequences
TL;DR: The above periodicities are the main hidden oscillating patterns detected so far in the genomic sequences, characteristic for the protein-coding sequences only.
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Measure representation and multifractal analysis of complete genomes
TL;DR: Spectral analyses performed indicate that these measure representations, considered as time series, exhibit strong long-range correlation and the multifractal property of the measure representation and the classification of bacteria.
Journal ArticleDOI
Long-range correlations in DNA
Journal ArticleDOI
Short-range Order in Two Eukaryotic Genomes: Relation to Chromosome Structure
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