Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.
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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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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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
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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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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TL;DR: In this article, two methods for defining Fourier power spectra for DNA sequences or other biological sequences are compared, and it is shown that the Fourier transform of the two methods are essentially the same.
Abstract: Two methods for defining Fourier power spectra for DNA sequences or other biological sequences are compared. The first method uses indicator sequences for each letter. The second method by Silverman and Linsker assigns to each letter a vertex of a regular tetrahedron in space, and this can be generalized to any dimension. While giving different Fourier transforms, it is shown that the power spectra of the two methods are essentially the same. This is also true if one replaces the Fourier transform in both methods with another linear transform, such as the Walsh transform.
47 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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TL;DR: A novel way to develop new and efficient codon indices by simultaneously characterizing the fractal and periodic features of a DNA sequence by studying all of the 16 yeast chromosomes is described.
Abstract: Most codon indices used today are based on highly biased nonrandom usage of codons in coding regions. The background of a coding or noncoding DNA sequence, however, is fairly random, and can be characterized as a random fractal. When a gene-finding algorithm incorporates multiple sources of information about coding regions, it becomes more successful. It is thus highly desirable to develop new and efficient codon indices by simultaneously characterizing the fractal and periodic features of a DNA sequence. In this paper, we describe a novel way of achieving this goal. The efficiency of the new codon index is evaluated by studying all of the 16 yeast chromosomes. In particular, we show that the method automatically and correctly identifies which of the three reading frames is the one that contains a gene.
40 citations
TL;DR: The isolation and characterization of an alpha-satellite subset specific for human chromosome 2 is described, organized as a series of diverged 680-bp tetramers, revealed after digestion of genomic DNA with HaeIII, HindIII, HinfI, StuI, and XbaI.
39 citations
TL;DR: No general statement can be made on the influence of coding and non-coding content on the correlation length of a given sequence, and the multifractal spectrum is shown to be more sensitive for detecting dependence structures within the DNA sequence than the averaged contribution given by redundancy.
Abstract: We present a generalization of the standard chaos-game representation method introduced by Jeffrey. To this aim, a DNA symbolic sequence is mapped onto a singular measure on the attractor of a particular IFS model, which is a perfect statistical representation of the sequence. A multifractal analysis of the resulting measure is introduced and an interpretation of singularities in terms of mutual information and redundancy (statistical dependence) among subsequence symbols within the DNA sequence is provided. The multifractal spectrum is also shown to be more sensitive for detecting dependence structures within the DNA sequence than the averaged contribution given by redundancy. This method presents several advantages with respect to other representations such as walks or interfaces, which may introduce spurious effects. In contrast with the results obtained by other standard methods, here we note that no general statement can be made on the influence of coding and non-coding content on the correlation length of a given sequence.
39 citations
TL;DR: In this paper, four parameters (distance, correlation coefficient, entropy and mutual information) are introduced to provide exact measures of the difference between a real genome and the white noise genome of it.
38 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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