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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18 citations
TL;DR: A conversion of the FTES signals to a common platform of Shannon information content to facilitate comparisons of periodic data with other measures of information for genes and genomes is described.
17 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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TL;DR: The analysis of cross correlations in the different ranges of structural spectra permits identification of the main sources of correlations, namely, the coherent point mutations, coincident periodicities or large scale density variations.
17 citations
14 Nov 2006
TL;DR: A new approach to reduce the computational burden associated with STFT computation, for coding regions detection purposes is presented and Experimental results show significant savings in computation time when the proposed algorithm is employed.
Abstract: Due to the non-uniform distribution of codons in coding regions, a three-periodicity is present in most of genome coding regions which, after a previous numeric conversion, show a notable peak at frequency component N/3 when calculating the Fourier Transform. Taking into account the veracity of this result, the Short Time Fourier Transform has been applied to large DNA sequences to predict coding regions. This paper presents a new approach to reduce the computational burden associated with STFT computation, for coding regions detection purposes. Experimental results show significant savings in computation time when the proposed algorithm is employed.
15 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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TL;DR: To further define the structure of the pericentromeric region of human chromosome 7, a YAC clone containing the D7S1480 locus is identified and characterized by linkage in CEPH families and radiation hybrid analysis.
Abstract: To further define the structure of the pericentromeric region of human chromosome 7, we have identified and characterized a YAC clone (YAC 311.H5) containing the D7S1480 locus, which maps to the short arm near the centromere of this chromosome, by linkage in CEPH families and radiation hybrid analysis. This YAC contains two new blocks of alphoid DNA (named Z5 and Z6). Both Z5 and Z6 show monomeric structures and a lack of higher-order repeats, and, therefore, belong to suprachromosomal family type 4 (M1). The orientation of the two blocks and the physical distances over the region were defined by pulsed-field gel electrophoresis (PFGE) and fluorescence in situ hybridization on chromatin fibers (FiberFISH). A YAC contig spanning the centromeric region has been developed by STS content.
13 citations