Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.
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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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Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation
TL;DR: The Spectral Repeat Finder program circumvents problems by using a discrete Fourier transformation to identify significant periodicities present in a sequence and shows efficient and complete detection of repeats.
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Changchuan Yin,Stephen S.-T. Yau +1 more
TL;DR: A new method to predict protein coding regions is developed based on the fact that most of exon sequences have a 3-base periodicity, while intron sequences do not have this unique feature.
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Statistical mechanics in biology: how ubiquitous are long-range correlations?
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TL;DR: The analysis of long-term data on human heartbeats that supports the possibility that the successive increments in the cardiac beat-to-beat intervals of healthy subjects display scale-invariant, long-range "anti-correlations", suggesting that the classical theory of homeostasis should be extended to account for this type of dynamical, far from equilibrium, behavior.
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Structure of the major block of alphoid satellite DNA on the human Y chromosome.
Chris Tyler-Smith,William Brown +1 more
TL;DR: The results provide a basis for further structural analysis of the human Y chromosome centromeric region, and suggest that long-range structural polymorphisms of tandemly repeated sequence families may be frequent.
Journal ArticleDOI
The gene identification problem: An overview for developers
TL;DR: The gene identification problem is the problem of interpreting nucleotide sequences by computer, in order to provide tentative annotation on the location, structure, and functional class of protein-coding genes, and the number of algorithm and software developers working in the area is rapidly increasing.