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
TL;DR: A review of the literature on statistical long-range correlation in DNA sequences can be found in this paper, where the authors conclude that a mixture of many length scales (including some relatively long ones) is responsible for the observed 1/f-like spectral component.
Measure representation and multifractal analysis of complete genomes
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Journal ArticleDOI
Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm
Matko Glunčić,Vladimir Paar +1 more
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Journal ArticleDOI
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 measure of DNA periodicity
B.D. Silverman,R. Linsker +1 more
TL;DR: The transform is invariant to the labelling of the bases and can therefore be used as a measure of periodicity for segments of DNA with differing base content and can also be conveniently used to search for base periodicities within large DNA data bases.
Journal ArticleDOI
Compositional segmentation and long-range fractal correlations in DNA sequences
TL;DR: A segmentation algorithm based on the Jensen-Shannon entropic divergence is used to decompose long-range correlated DNA sequences into statistically significant, compositionally homogeneous patches, demonstrating that neither the internal structure of patches nor the order in which these are arranged in the sequence is critical; therefore, long- range correlations in nucleotide sequences seem to rely only on the power-law distribution of patch lengths.
Journal ArticleDOI
Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: a survey of alphoid sequences from different human chromosomes
TL;DR: Based on the analysis of sequence variation at each position within the 171 basepair monomer, a consensus sequence is derived which is suggested to reflect the monomer sequence from which different chromosomal subsets have evolved.
Book
Advanced Engineering Mathematics
TL;DR: In this paper, the Laplace Transform is used to approximate the number of solutions of a linear system of differential equations, and the Fourier series and integral transform are used to solve the problem.
Journal ArticleDOI
Organization of human and mouse skeletal myosin heavy chain gene clusters is highly conserved.
Allison Weiss,Debra McDonough,Brett Wertman,Leslie Acakpo-Satchivi,Kate Montgomery,Raju Kucherlapati,Leslie A. Leinwand,Kenneth Krauter +7 more
TL;DR: High-resolution physical maps of both human and mouse loci using PCR-based marker content mapping of P1-artificial chromosome clones reveal that the order, transcriptional orientation, and relative intergenic distances of these genes are remarkably conserved between these species.