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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Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription.
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References
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Journal ArticleDOI
Fourier and Wavelet Transform Analysis, a Tool for Visualizing Regular Patterns in DNA Sequences
TL;DR: A correlation function that compares each base in a DNA sequence to its various neighbours and which is subsequently processed by Fourier and wavelet transforms has been developed and permits to readily visualize regular features in DNA which are related to the stability of heteroduplexes formed upon strand slippage.
Journal ArticleDOI
Chromosome-specific subfamilies within human alphoid repetitive DNA.
TL;DR: The expected presence of only one or a few distinct subfamilies on individual chromosomes is supported by the study of the nucleotide sequence of 17 cloned fragments of alphoid repetitive DNA from chromosome 7, which all contain the characteristic pattern of 36 common nucleotide changes that defines one of the subfam families described.
Journal ArticleDOI
Measure representation and multifractal analysis of complete genomes
TL;DR: In this paper, a measure representation of DNA sequences is proposed and spectral analysis and multifractal analysis are performed on the measure representations of a large number of complete genomes, and it is concluded that these complete genomes are not random sequences.
Journal ArticleDOI
Finite sample effects in sequence analysis
TL;DR: In this paper, it is shown that entropy calculations are seriously affected by systematic errors due to the finite size of the samples, and that these difficulties can be dealt with by assuming simple probability distributions underlying the generating process (e.g. equidistribution, power-law distribution, exponential distribution).