41 research outputs found
Multifractal characterisation of length sequences of coding and noncoding segments in a complete genome
The coding and noncoding length sequences constructed from a complete genome
are characterised by multifractal analysis. The dimension spectrum and
its derivative, the 'analogous' specific heat , are calculated for the
coding and noncoding length sequences of bacteria, where is the moment
order of the partition sum of the sequences. From the shape of the
and curves, it is seen that there exists a clear difference between the
coding/noncoding length sequences of all organisms considered and a completely
random sequence. The complexity of noncoding length sequences is higher than
that of coding length sequences for bacteria. Almost all curves for
coding length sequences are flat, so their multifractality is small whereas
almost all curves for noncoding length sequences are multifractal-like.
We propose to characterise the bacteria according to the types of the
curves of their noncoding length sequences.Comment: 15 pages with 5 figures, Latex, Accepted for publication in Physica
Measure representation and multifractal analysis of complete genomes
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 spectra and related 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. For substrings with length K=8, the
spectra of all organisms studied are multifractal-like and sufficiently smooth
for the curves to be meaningful. The curves of all bacteria
resemble a classical phase transition at a critical point. But the 'analogous'
phase transitions of chromosomes of non-bacteria organisms are different. Apart
from Chromosome 1 of {\it C. elegans}, they exhibit the shape of double-peaked
specific heat function.Comment: 12 pages with 9 figures and 1 tabl
Preparation and use of maize tassels’ activated carbon for the adsorption of phenolic compounds in environmental waste water samples
The determination and remediation of three phenolic compounds bisphenol A (BPA), ortho-nitrophenol (o-NTP), parachlorophenol (PCP) in wastewater is reported. The analysis of these molecules in wastewater was done using gas chromatography (GC) × GC time-of-flight mass spectrometry while activated carbon derived from maize tassel was used as an adsorbent. During the experimental procedures, the effect of various parameters such as initial concentration, pH of sample solution, eluent volume, and sample volume on the removal efficiency with respect to the three phenolic compounds was studied. The results showed that maize tassel produced activated carbon (MTAC) cartridge packed solid-phase extraction (SPE) system was able to remove the phenolic compounds effectively (90.84–98.49 %, 80.75–97.11 %, and 78.27–97.08 % for BPA, o-NTP, and PCP, respectively) . The MTAC cartridge packed SPE sorbent performance was compared to commercially produced C18 SPE cartridges and found to be comparable. All the parameters investigated were found to have a notable influence on the adsorption efficiency of the phenolic compounds from wastewaters at different magnitudes
Clustering of Protein Structures Using Hydrophobic Free Energy And Solvent Accessibility of Proteins
Iterated Function System and Multifractional Analysis of Biological Sequences
The fractal method has been successfully used to study many problems in physics, mathematics, engineering, finance, even in biology till now. In the past decade or so there has been a ground swell of interest in unravelling the mysteries of DNA. How to get more bioinformations from these DNA sequences is a challenging problem. The problem of classification and evolution relationship of organisms are the central problems in bioinformatics. And it is also very hard to predict the secondary and space structure of a protein from its amino acid sequence. In this paper, some recent results related these problems obtained through multifractal analysis and iterated function system (IFS) model are introduced
Chaos Game Representation of Protein Sequences Based on the Detailed HP Model and their Multifractal and Correlation Analyses
Similar to the chaos game representation (CGR) of DNA sequences proposed by Jeffrey (Nucleic Acid Res. 18 (1990) 21 63), a new CGR of protein sequences based on the detailed HP model is proposed. Multifractal and correlation analyses of the measures based on the CGR of protein sequences from complete genomes are performed. The Dq spectra of all organisms studied are multifractal-like and sufficiently smooth for the Cq curves to be meaningful. The Cq curves of bacteria resemble a classical phase transition at a critical point. The correlation distance of the different between the measure based on the CGR of protein sequences and its fractal background is also proposed to construct a more precise phylogenetic tree of bacteria