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

doi:10.1186/1471-2105-9-466

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

Journal Article•DOI•

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

Vladimir Paar¹, Nenad Pavin², Ivan Basar¹, Marija Rosandić¹, Matko Glunčić¹, Nils Paar¹ - Show less +2 more•Institutions (2)

University of Zagreb¹, Max Planck Society²

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.

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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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Book•DOI•

Data Mining Techniques for the Life Sciences

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Oliviero Carugo, Frank Eisenhaber

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.

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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.

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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 Article•DOI•

Understanding Long-range Correlations in DNA Sequences

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Wentian Li¹, Thomas G. Marr¹, Kunihiko Kaneko²•Institutions (2)

Cold Spring Harbor Laboratory¹, University of Tokyo²

22 Mar 1994-arXiv: Chaotic Dynamics

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.

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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.

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130 citations

Measure representation and multifractal analysis of complete genomes

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Zu-Guo Yu¹, Zu-Guo Yu², Vo Anh², Ka-Sing Lau³•Institutions (3)

Xiangtan University¹, Queensland University of Technology², The Chinese University of Hong Kong³

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.

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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}).

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102 citations

Journal Article•DOI•

Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

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Matko Glunčić¹, Vladimir Paar¹•Institutions (1)

University of Zagreb¹

01 Jan 2013-Nucleic Acids Research

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.

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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).

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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 Article•DOI•

Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription.

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G.I. Kravatskaya¹, Y. V. Kravatsky¹, V. R. Chechetkin¹, Vladimir G. Tumanyan¹•Institutions (1)

Engelhardt Institute of Molecular Biology¹

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.

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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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Journal Article•DOI•

Functional and evolutionary roles of long repeats in prokaryotes

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Eduardo P. C. Rocha¹, Eduardo P. C. Rocha², Antoine Danchin¹, Alain Viari²•Institutions (2)

Pasteur Institute¹, University of Paris²

01 Nov 1999-Research in Microbiology

TL;DR: The various functional and evolutionary roles of long strict repeats are discussed, focusing in particular on their role in terms of genome stability, gene transfer, and antigenic variation.

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59 citations

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

...Repeat sequences are a common feature of genomes [1-3]....
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Journal Article•DOI•

Search of hidden periodicities in DNA sequences.

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V. R. Chechetkin, A. Yu. Turygin

21 Aug 1995-Journal of Theoretical Biology

TL;DR: The methods applied to the structural analysis of genome for bacteriophage PHIX174 indicate the important role of the coherent structural modifications along the several main periods in the formation of the genome.

...read moreread less

58 citations

Journal Article•DOI•

Long-range fractal correlations in DNA.

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Sergey V. Buldyrev¹, Sergey V. Buldyrev², Sergey V. Buldyrev³, Ary L. Goldberger², Ary L. Goldberger³, Ary L. Goldberger¹, Shlomo Havlin², Shlomo Havlin³, Shlomo Havlin¹, Chung-Kang Peng², Chung-Kang Peng³, Chung-Kang Peng¹, Michael Simons², Michael Simons³, Michael Simons¹, Francesco Sciortino¹, Francesco Sciortino³, Francesco Sciortino², H. E. Stanley², H. E. Stanley³, H. E. Stanley¹ - Show less +17 more•Institutions (3)

Harvard University¹, Massachusetts Institute of Technology², Boston University³

13 Sep 1993-Physical Review Letters

57 citations

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

...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 Article•DOI•

Statistical analysis of the DNA sequence of human chromosome 22.

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Dirk Holste¹, Ivo Grosse², Hanspeter Herzel¹•Institutions (2)

Humboldt University of Berlin¹, Cold Spring Harbor Laboratory²

26 Sep 2001-Physical Review E

TL;DR: The presence of interspersed repeats may cause the sublinear increase of H(n) with n, and that the presence of monomeric tandem repeats as well as the suppression of CG dinucleotides maycause the observed decay of H (n)(q) with q.

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Abstract: We study statistical patterns in the DNA sequence of human chromosome 22, the first completely sequenced human chromosome. We find that (i). the 33.4 x 10(6) nucleotide long human chromosome exhibits long-range power-law correlations over more than four orders of magnitude, (ii). the entropies H(n) of the frequency distribution of oligonucleotides of length n (n-mers) grow sublinearly with increasing n, indicating the presence of higher-order correlations for all of the studied lengths 1

...read moreread less

56 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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...With the availability of large sequences and extended statistical computations, showing power-law correlations over four or five orders of magnitude, with exponents which are consistent with previous results obtained analyzing short sequences, such correlations in human DNA, with fractal-like scaling, are now commonly accepted [27,28,45]....
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Journal Article•DOI•

An efficient method for matching nucleic acid sequences

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Joseph Felsenstein, Stanley Sawyer¹, Rochelle Kochin²•Institutions (2)

Purdue University¹, University of Washington²

11 Jan 1982-Nucleic Acids Research

TL;DR: Though the objective achieved is of limited interest, this method will complement algorithms for efficiently finding the longest matching parts of two sequences, and is faster than existing algorithms for finding matches allowing deletions and insertions.

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Abstract: A method of computing the fraction of matches between two nucleic acid sequences at all possible alignments is described. It makes use of the Fast Fourier Transform. It should be particularly efficient for very long sequences, achieving its result in a number of operations proportional to n ln n, where n is the length of the longer of the two sequences. Though the objective achieved is of limited interest, this method will complement algorithms for efficiently finding the longest matching parts of two sequences, and is faster than existing algorithms for finding matches allowing deletions and insertions. A variety of economies can be achieved by this Fast Fourier Transform technique in matching multiple sequences, looking for complementarity rather than identity, and matching the same sequences both in forward and reversed orientations.

...read moreread less

55 citations

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

...Spectral analysis employing Discrete Fourier transform is used to reveal periodicity in symbolic sequences, like genomic and protein sequences [7,9,14,16,17,20,36-53], to investigate long-range correlations [4,5,54,55] and to study the problem of sequence similarity [14,56-62]....
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