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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BookDOI
Data Mining Techniques for the Life Sciences
Oliviero Carugo,Frank Eisenhaber +1 more
TL;DR: "Data Mining Techniques for the Life Sciences" seeks to aid students and researchers in the life sciences who wish to get a condensed introduction into the vital world of biological databases and their many applications.
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Understanding Long-range Correlations in DNA Sequences
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Measure representation and multifractal analysis of complete genomes
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Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm
Matko Glunčić,Vladimir Paar +1 more
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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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Journal ArticleDOI
A fractal method to distinguish coding and non-coding sequences in a complete genome based on a number sequence representation.
TL;DR: A fractal method to distinguish coding and non-coding sequences in a complete genome is proposed, based on different statistical behaviors between these two kinds of sequences.
Journal ArticleDOI
Information decomposition of symbolic sequences
TL;DR: In this paper, a non-parametric method of information decomposition of any symbolical sequence is proposed, based on the calculation of Shannon mutual information between analyzed and artificial symbolical sequences.
Journal ArticleDOI
Random Two-Component One-Dimensional Ising Model for Heteropolymer Melting
TL;DR: In this paper, a leading-order approximation for an additive physical quantity in the melting region is introduced; it is intimately connected with the microscopic statistical herteropolymer structure, which allows one to derive the heteropolymer distribution function (over the length and composition of the sections) directly from experimental data.
Book
Human genome evolution
TL;DR: Mutational processes in pathology and evolution, M. Krawczak and D.N. Patthy Evolution of the HLA complex, A.L. Hughes and S. Hughes evolution of the G-protein coupled receptor superfamily.
Journal ArticleDOI
Analysis of Apparent 1/fα Spectrum in DNA Sequences
TL;DR: The question whether the correlations in DNA sequences are long ranged or short ranged is addressed by an extensive analysis of genetic sequences and the results do not support the notion of critical properties of sequential distribution of nucleotides.