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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Book ChapterDOI
Numerical Representations in Alpha Satellite DNA Analysis
G. P. Pop,E. Onaca +1 more
TL;DR: The application of spectrograms using different DNA numerical representations to identify alpha satellite higher order repeats is investigated.
Proceedings ArticleDOI
Spectral analysis of alpha satellite DNA
TL;DR: Results obtained by combining grey level spectrograms with two numerical representations to isolate position and length of DNA repeats from human alpha satellite DNA are presented.
References
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TL;DR: The sequence of the euchromatic part of human chromosome 22 is reported, which consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.
Journal ArticleDOI
Recognition of protein coding regions in DNA sequences
TL;DR: The test has been thoroughly proven on 400,000 bases of sequence data: it misclassifies 5% of the regions tested and gives an answer of "No Opinion" one fifth of the time.
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Giorgio Bernardi,Birgitta Olofsson,Jan Filipski,Marino Zerial,Julio Salinas,Gérard Cuny,Michele Meunier-Rotival,Francis Rodier +7 more
TL;DR: This approach has revealed that the distribution of genes, integrated viral sequences, and interspersed repeats is highly nonuniform in the genome, and that the base composition and ratio of CpG to GpC in both coding and noncoding sequences, as well as codon usage, mainly depend on the GC content of the isochores harboring the sequences.