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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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Journal ArticleDOI
29 Jan 1993-Science
TL;DR: The mosaic character of DNA consisting of patches of different composition can fully account for apparent long-range correlations in DNA.
Abstract: The highly nonrandom character of genomic DNA can confound attempts at modeling DNA sequence variation by standard stochastic processes (including random walk or fractal models). In particular, the mosaic character of DNA consisting of patches of different composition can fully account for apparent long-range correlations in DNA.

188 citations


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

  • ...It has been pointed out that the mosaic structure of genome is presumably responsible for long-range correlations [79,85,86]....

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  • ...The lack of long enough sequences and the use of different methods of estimating the correlations, leading to some results not strictly comparable to each other contributed to controversies regarding findings on long-range correlations, like the presence of these correlations only in non-coding or in all human genomic sequences, and their presence in other organisms [5,6,23,36,78-83]....

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Journal ArticleDOI
TL;DR: It is proposed that homogenization of AS may be limited to arrays participating in centromeric function, and after the establishment of the new arrays homogenized in the old arrays stopped.
Abstract: In this report we review alpha-satellite DNA (AS) sequence data to support the following proposed scenario of AS evolution. Centromeric regions of lower primate chromosomes have solely "old" AS based on type A monomeric units. Type A AS is efficiently homogenized throughout the whole genome and is nearly identical in all chromosomes. In the ancestors of great apes, a divergent variant of the type A monomer acquired the ability to bind CENP-B protein and expanded in the old arrays, mixing irregularly with type A. As a result, a new class of monomers, called type B, was formed. The "new" AS families were established by amplification of divergent segments of irregular A-B arrays and spread to many chromosomes before the human-chimpanzee-gorilla split. The new arrays contain regularly alternating monomers of types A and B. New AS is homogenized within an array with little or no homogenization between chromosomes. Most human chromosomes contain only one new array and one or a few old arrays. However, as a rule only new arrays are efficiently homogenized. Apparently, in evolution, after the establishment of the new arrays homogenization in the old arrays stopped. Notably, kinetochore structures marking functional centromeres are also usually formed on the new arrays. We propose that homogenization of AS may be limited to arrays participating in centromeric function.

177 citations


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

  • ...Alphoid arrays consist of tandem repeats of alpha satellite monomer unit of approximately 171 bp, which form chromosome-specific higher order repeats (HOR) or monomeric organization consisting of diverged monomers [90-104]....

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  • ...morphic variation within these subsets [90-103]....

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Journal ArticleDOI
TL;DR: The role of digital filtering techniques in gene identification and the topic of long-range correlation between base pairs in DNA sequences, which corresponds to a 1/f type of power spectrum are reviewed.
Abstract: With the enormous amount of genomic and proteomic data that is available to us in the public domain, it is becoming increasingly important to be able to process this information in ways that are useful to humankind. Signal processing methods have played an important role in this context, some of which are reviewed in this paper. First we review the role of digital filtering techniques in gene identification. We then discuss the topic of long-range correlation between base pairs in DNA sequences. This correlation corresponds to a 1/f type of power spectrum. We also describe some of the recent applications of Fourier methods in the study of proteins. Finally we mention the role of Karhunen-Loeve like transforms in the interpretation of DNA microarray data for gene expression.

175 citations

Journal ArticleDOI
TL;DR: It is shown that, in sequences over an alphabet of λ symbols, statistical dependences are measured by (λ − 1)2 independent parameters, however, not all of them can be determined by autocorrelation functions.
Abstract: The paper is devoted to relations between correlation functions and mutual information. It is shown that, in sequences over an alphabet of λ symbols, statistical dependences are measured by (λ − 1)2 independent parameters. However, not all of them can be determined by autocorrelation functions. Appropriate sets of correlation functions (including crosscorrelations) are introduced, which allow the detection of all dependences. The results are exemplified for binary, ternary, and quaternary symbol sequences. As an application, it is discussed that a nonuniform codon usage in protein-coding DNA sequences introduces periodic correlations even at distances in the order of 1000 base pairs.

173 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: The sequences in the vicinity of the centromere that are included in the current genome assembly are described, the approximately 7Mb of alpha satellite that have been assembled thus far are analyzed and the nature of the sequences that remain to be accounted for are anticipated.

170 citations


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

  • ...Alphoid arrays consist of tandem repeats of alpha satellite monomer unit of approximately 171 bp, which form chromosome-specific higher order repeats (HOR) or monomeric organization consisting of diverged monomers [90-104]....

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  • ...In [104] 16 mers were identified by DOTTER analysis; the presence of 16 mer was reported, but detailed HOR structure was not presented....

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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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