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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References
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Journal ArticleDOI
Characterizing long-range correlations in DNA sequences from wavelet analysis.
TL;DR: The wavelet transform microscope is demonstrated and quantify the existence of long-range correlations in genes containing introns and noncoding regions, and the fluctuations in the patchy landscapes of DNA walks are found to be homogeneous with Gaussian statistics.
Journal ArticleDOI
Synergy between sequence and size in Large-scale genomics
TL;DR: Until recently the study of individual DNA sequences and of total DNA content (the C-value) sat at opposite ends of the spectrum in genome biology, but the dawn of comprehensive genome sequencing has allowed a new synergy between these fields, with sequence data providing novel insights into genome- size evolution, and with genome-size data being of both practical and theoretical significance for large-scale sequence analysis.
Journal ArticleDOI
Z Curves, An Intutive Tool for Visualizing and Analyzing the DNA Sequences
Ren Zhang,Chun-Ting Zhang +1 more
TL;DR: The study of the Z curves develops further a new area to visualizing and analyzing the DNA sequences by a geometrical approach by using the ripe mathematical tools of geometry and the powerful technique of the computer graphics.
Journal ArticleDOI
Frequency-domain analysis of biomolecular sequences
TL;DR: An optimization procedure improving upon traditional Fourier analysis performance in distinguishing coding from noncoding regions in DNA sequences is provided and it is demonstrated that color spectrograms can visually provide significant information about biomolecular sequences, thus facilitating understanding of local nature, structure and function.
Journal ArticleDOI
Computational prediction of eukaryotic protein-coding genes
TL;DR: Computational prediction approaches have proliferated in recent years that predict the location and structure of genes and why they have become essential for the analyses of newly sequenced genomes.