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Journal ArticleDOI

Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.

03 Nov 2008-BMC Bioinformatics (BioMed Central)-Vol. 9, Iss: 1, pp 466-466
TL;DR: 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.

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Citations
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BookDOI
14 Dec 2009
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.
Abstract: Whereas getting exact data about living systems and sophisticated experimental procedures have primarily absorbed the minds of researchers previously, the development of high-throughput technologies has caused the weight to increasingly shift to the problem of interpreting accumulated data in terms of biological function and biomolecular mechanisms. In "Data Mining Techniques for the Life Sciences", experts in the field contribute valuable information about the sources of information and the techniques used for "mining" new insights out of databases. Beginning with a section covering the concepts and structures of important groups of databases for biomolecular mechanism research, the book then continues with sections on formal methods for analyzing biomolecular data and reviews of concepts for analyzing biomolecular sequence data in context with other experimental results that can be mapped onto genomes. As a volume of the highly successful Methods in Molecular Biology series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Authoritative and easy to reference, "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.

135 citations


Cites background or methods from "Hierarchical structure of cascade o..."

  • ...More recently, new technologies of third and fourth generation sequencing [5] such as single cell molecule [6], nanopore-based [7] have been applied to whole-transcriptome analysis that opened a possibility for profiling rare or heterogeneous populations of cells....

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  • ...The frequency of stabilizing and destabilizing mutations in all single mutants [5] showed that most of the mutational experiments have been carried out with hydrophobic substitutions (replacement of one hydrophobic residue with another, e....

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  • ...The stability data for a set of 180 double mutants have been collected from ProTherm database [3, 5] and related them with sequence based features such as wild-type residue, mutant residue, and three neighboring residues on both directions of the mutant site....

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  • ...org/) [5], with the aim of coordinating and synchronizing the curation effort of all the participants and to offer a unified, freely available, consistently annotated and nonredundant molecular interaction dataset....

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  • ...The data come in three different formats: old-style PDB-format files, macromolecular Crystallographic Information File (mmCIF) format [5], and a XMLstyle format called PDBML/XML [6]....

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Journal ArticleDOI
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.
Abstract: In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones) in DNA sequences is responsible for the observed 1/f-like spectral component. We note the complexity of the correlation structure in DNA sequences. The observed complexity often makes it hard, or impossible, to decompose the sequence into a few statistically stationary regions. We suggest that, based on the complexity of DNA sequences, a fruitful approach to understand long-range correlation is to model duplication, and other rearrangement processes, in DNA sequences. One model, called ``expansion-modification system", contains only point duplication and point mutation. Though simplistic, this model is able to generate sequences with 1/f spectra. We emphasize the importance of DNA duplication in its contribution to the observed long-range correlation in DNA sequences.

130 citations

01 Aug 2001
TL;DR: Spectral analyses performed indicate that these measure representations, considered as time series, exhibit strong long-range correlation and the multifractal property of the measure representation and the classification of bacteria.
Abstract: This paper introduces the notion of measure representation of DNA sequences. Spectral analysis and multifractal analysis are then performed on the measure representations of a large number of complete genomes. The main aim of this paper is to discuss the multifractal property of the measure representation and the classification of bacteria. From the measure representations and the values of the Dq spectra and related Cq curves, it is concluded that these complete genomes are not random sequences. In fact, spectral analyses performed indicate that these measure representations, considered as time series, exhibit strong long-range correlation. Here the long-range correlation is for the K-strings with dictionary ordering, and it is different from the base pair correlations introduced by other people. For substrings with length K=8, the Dq spectra of all organisms studied are multifractal-like and sufficiently smooth for the Cq curves to be meaningful. With the decreasing value of K, the multifractality lessens. The Cq curves of all bacteria resemble a classical phase transition at a critical point. But the ‘‘analogous’’ phase transitions of chromosomes of nonbacteria organisms are different. Apart from chromosome 1 of C. elegans, they exhibit the shape of double-peaked specific heat function. A classification of genomes of bacteria by assigning to each sequence a point in two-dimensional space (D_{-1} ,D1) and in three-dimensional space (D_{-1} ,D1 ,D_{-2}) was given. Bacteria that are close phylogenetically are almost close in the spaces (D_{-1} ,D1) and (D_{-1} ,D1 ,D_{-2}).

102 citations

Journal ArticleDOI
TL;DR: This work presents several case studies of GRM use, and presents the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram.
Abstract: The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012 .exe) is its ability to identify a broad variety of repeats of unbounded length that can be arbitrarily distant in sequences as large as human chromosomes. The efficacy is due to the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram. In this way, we obtain very fast, efficient and highly automatized repeat finding tool. The method is robust to substitutions and insertions/deletions, as well as to various complexities of the sequence pattern. We present several case studies of GRM use, in order to illustrate its capabilities: identification of a-satellite tandem repeats and higher order repeats (HORs), identification of Alu dispersed repeats and of Alu tandems, identification of Period 3 pattern in exons, implementation of ‘magnifying glass’ effect, identification of complex HOR pattern, identification of inter-tandem transitional dispersed repeat sequences and identification of long segmental duplications. GRM algorithm is convenient for use, in particular, in cases of large repeat units, of highly mutated and/ or complex repeats, and of global repeat maps for large genomic sequences (chromosomes and genomes).

27 citations


Cites result from "Hierarchical structure of cascade o..."

  • ...These GRM results are in accordance with the pattern of previous results obtained by using heuristic algorithms (96)....

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Journal ArticleDOI
01 Sep 2011-Genomics
TL;DR: The comparison with available experimental data indicates that promoters with the most pronounced periodicities may be related to the supercoiling-sensitive genes.

23 citations


Cites background from "Hierarchical structure of cascade o..."

  • ...This sum is invariant with respect to complementary inversion of a sequence [34] and is more convenient for comparing the helical periodicities in the complete genome and in the promoter sequences (in the latter case, the promoters on two chains were always compiled as 5 ́–3 ́ sequences)....

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  • ...through sets of equidistant peaks [31, 34, 35]....

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References
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Proceedings ArticleDOI
17 Jul 2005
TL;DR: This work proposes a method for finding hidden periodicities in DNA based on Fourier analysis that is effective for finding new repeat patterns that were previously undetected by some of the most popular algorithms published in the literature.
Abstract: Finding repetitive sequences in DNA is of particular interest in biology due to their role in genetic diseases, human gene mapping, evolution, and many other important and interesting applications. We propose a method for finding hidden periodicities in DNA based on Fourier analysis. It is shown that this approach is effective for finding new repeat patterns that were previously undetected by some of the most popular algorithms published in the literature

22 citations


"Hierarchical structure of cascade o..." refers methods in this paper

  • ...A single binary sequence was used by mapping genomic sequence into purine/pyrimidine representation [22], or into weak bond/strong bond representation [109]....

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Proceedings ArticleDOI
17 May 2004
TL;DR: An evolutionary force heuristic is proposed to merge interspersed perfect tandem repeat sequences into an ATR structure and a more general method is presented using a product spectrum of Fourier nucleotide subsequences to detect hidden periodicity.
Abstract: The detection of tandem repeats is important in biology and medicine as it can be used for phylogenetic studies and disease diagnosis. The paper proposes two techniques for detecting approximate tandem repeats (ATRs) in DNA sequences. First, an evolutionary force heuristic is proposed to merge interspersed perfect tandem repeat sequences into an ATR structure. Next., a more general method is presented using a product spectrum of Fourier nucleotide subsequences to detect hidden periodicity. The Fourier method is sensitive to ATRs and is robust in the presence of substitutions, insertions, and deletions.

22 citations


"Hierarchical structure of cascade o..." refers background or methods in this paper

  • ...A peak at a frequency f in Fourier power spectrum of base correlations of a given genomic sequence shows a kind of l = 1/f – base periodicity, exact or approximate [14-16,63]....

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  • ...Different computational techniques have been used: Fourier spectral analysis [4-20], wavelet transform [21], DNA walk analysis [22-25], information theory measures [26-28], informational decomposition [29,30], quaternionic periodicity transform [31], exactly periodic subspace decomposition [32,33], portrait method [34], enhance algorithm for distance frequency distribution [35], etc....

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Journal ArticleDOI
TL;DR: In this article, correlation properties of ∼7500 gene sequences, covering coding (exon) and non-coding (intron) sequences for DNA and primary amino acid sequences for proteins, across all three domains of life, namely Eukaryotes (cells with nuclei), Prokaryote (bacteria) and Archaea (archaebacteria).

22 citations


"Hierarchical structure of cascade o..." refers methods in this paper

  • ...Different computational techniques have been used: Fourier spectral analysis [4-20], wavelet transform [21], DNA walk analysis [22-25], information theory measures [26-28], informational decomposition [29,30], quaternionic periodicity transform [31], exactly periodic subspace decomposition [32,33], portrait method [34], enhance algorithm for distance frequency distribution [35], etc....

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Journal ArticleDOI
TL;DR: Its application to DNA subtelomeric sequences from two lower eukaryotes, P.falciparum and S.cerevisiae, reveals ordered patterns organised in hierarchical periodicities, not easily recognizable by other methods.
Abstract: A method is proposed for the automatic detection of serial periodicities in a linear sequence. Its application to DNA subtelomeric sequences from two lower eukaryotes, P.falciparum and S.cerevisiae, reveals ordered patterns organised in hierarchical periodicities, not easily recognizable by other methods. The possible implications concerning the evolution of tandemly repetitive arrays are discussed in light of a model which involves, as successive steps, random repeat modification, the fusion of differently modified repeat versions into longer units, and the amplification of (and/or homogenization to) the more recent repeat units.

22 citations


"Hierarchical structure of cascade o..." refers methods in this paper

  • ...Different computational techniques have been used: Fourier spectral analysis [4-20], wavelet transform [21], DNA walk analysis [22-25], information theory measures [26-28], informational decomposition [29,30], quaternionic periodicity transform [31], exactly periodic subspace decomposition [32,33], portrait method [34], enhance algorithm for distance frequency distribution [35], etc....

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Journal ArticleDOI
TL;DR: A graphical user interface method, ColorHOR, is developed, based on an extension of the key-string algorithm, for fast computational identification of HORs in a given genomic sequence, without requiring a priori information on the composition of the genomic sequence.
Abstract: Motivation: GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR consensus lengths have not been reported so far. Given the fast growth of sequence databases in the centromeric region, it is of increasing interest to have efficient tools for computational identification and analysis of HORs from known sequences. Results: We develop a graphical user interface method, ColorHOR, for fast computational identification of HORs in a given genomic sequence, without requiring a priori information on the composition of the genomic sequence. ColorHOR is based on an extension of the key-string algorithm and provides a color representation of the order and orientation of HORs. For the key string, we use a robust 6 bp string from a consensus alpha satellite and its representative nature is tested. ColorHOR algorithm provides a direct visual identification of HORs (direct and/or reverse complement). In more detail, we first illustrate the ColorHOR results for human chromosome 1. Using ColorHOR we determine for the first time the HOR annotation of the GenBank sequence of the whole human genome. In addition to some HORs, corresponding to those determined previously biochemically, we find new HORs in chromosomes 4, 8, 9, 10, 11 and 19. For the first time, we determine exact consensus lengths of HORs in 10 chromosomes. We propose that the HOR assignment obtained by using ColorHOR be included into the GenBank database. Availability: The program with graphical user interface application for ColorHOR is freely available at http://www.hazu.hr/KSA/colorHOR.html. It can be run on any platform on which wxPython is supported. Contact: [email protected] Supplementary information:http://www.hazu.hr/KSA/colorHOR.html.

22 citations


"Hierarchical structure of cascade o..." refers background in this paper

  • ...8 in chromosome 7, studied in Figures 1, 2, 3, 4, is characterized by a low divergence among 54 HOR copies in the sequence of only a few percent [105-108]....

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  • ...5), the 46 complete and 14 incomplete copies of 16 mer alphoid HOR were identified in the central domain (positions 31338 to 177434, total length 148147 bp) [105-107]....

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  • ...Recently, HORs and monomeric alpha satellites have been studied by computational analysis of genomic sequences from the NCBI genome assembly [104-108]....

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