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