Spectral Analysis of Guanine and Cytosine Fluctuations of Mouse Genomic DNA

We study global fluctuations of the guanine and cytosine base content (GC%) in mouse genomic DNA using spectral analyses. Power spectra S(f) of GC% fluctuations in all nineteen autosomal and two sex chromosomes are observed to have the universal functional form S(f) \sim 1/f^alpha (alpha \approx 1) over several orders of magnitude in the frequency range 10^-7< f < 10^-5 cycle/base, corresponding to long-ranging GC% correlations at distances between 100 kb and 10 Mb. S(f) for higher frequencies (f > 10^-5 cycle/base) shows a flattened power-law function with alpha < 1 across all twenty-one chromosomes. The substitution of about 38% interspersed repeats does not affect the functional form of S(f), indicating that these are not predominantly responsible for the long-ranged multi-scale GC% fluctuations in mammalian genomes. Several biological implications of the large-scale GC% fluctuation are discussed, including neutral evolutionary history by DNA duplication, chromosomal bands, spatial distribution of transcription units (genes), replication timing, and recombination hot spots.Comment: 15 pages (figures included), 2 figure

Complexity on Acute Myeloid Leukemia mRNA Transcript Variant

This paper deals with the sequence analysis of acute myeloid leukemia mRNA. Six transcript variants of mlf1 mRNA, with more than 2000 bps, are analyzed by focusing on the autocorrelation of each distribution. Through the correlation matrix, some patches and similarities are singled out and commented, with respect to similar distributions. The comparison of Kolmogorov fractal dimension will be also given in order to classify the six variants. The existence of a fractal shape, patterns, and symmetries are discussed as well

Entropy and Multi-Fractality for the Myeloma Multiple TET 2 gene

The nucleotide and amino-acid distributions are studied for two variants of mRNA of gene that codes for a protein which is involved in multiple myeloid. Some patches and symmetries are singled out, thus, showing some distinctions between the two variants. Fractal dimensions and entropy are discussed as well

α-stable laws for noncoding regions in DNA sequences

In this work, we analyze the long-range dependence parameter for a nucleotide sequence in several different transformations. The long-range dependence parameter is estimated by the approximated maximum likelihood method, by a novel estimator based on the spectral envelope theory, by a regression method based on the periodogram function, and also by the detrended fluctuation analysis method. We study the length distribution of coding and noncoding regions for all Homo sapiens chromosomes available from the European Bioinformatics Institute. The parameter of the tail rate decay is estimated by the Hill estimator αˆ. We show that the tail rate decay is greater than 2 for coding regions, while for almost all noncoding regions it is less than 2.info:eu-repo/semantics/publishedVersio

Entropy and Multifractality for the Myeloma Multiple TET 2 Gene

The nucleotide and amino-acid distributions are studied for two variants of mRNA of gene that codes for a protein which is involved in multiple myeloid. Some patches and symmetries are singled out, thus, showing some distinctions between the two variants. Fractal dimensions and entropy are discussed as well

Genome analysis with inter-nucleotide distances

Motivation: DNA sequences can be represented by sequences of four symbols, but it is often useful to convert the symbols into real or complex numbers for further analysis. Several mapping schemes have been used in the past, but they seem unrelated to any intrinsic characteristic of DNA. The objective of this work was to find a mapping scheme directly related to DNA characteristics and that would be useful in discriminating between different species. Mathematical models to explore DNA correlation structures may contribute to a better knowledge of the DNA and to find a concise DNA description

Fractals and Hidden Symmetries in DNA

This paper deals with the digital complex representation of a DNA sequence and the analysis of existing correlations by wavelets. The symbolic DNA sequence is mapped into a nonlinear time series. By studying this time series the existence of fractal shapes and symmetries will be shown. At first step, the indicator matrix enables us to recognize some typical patterns of nucleotide distribution. The DNA sequence, of the influenza virus A (H1N1), is investigated by using the complex representation, together with the corresponding walks on DNA; in particular, it is shown that DNA walks are fractals. Finally, by using the wavelet analysis, the existence of symmetries is proven

Automatic Growth Detection of Cell Cultures through Outlier Techniques using 2D Images

Using conventional statistics, we have developed a new method for cell culture analysis through outlier detection techniques. Statistical methods enable researchers in microbiology to identify experimental parameters that are critical for colony growth and inhibition. This paper reports a method for analysing 2D images of cell cultures in Petri dishs, such as fungi, bacteria or yeast. The aim of this study was to obtain a sensitive and robust method for detection of growth rate, surface coverage and the approximate number of cells in the colony. For testing we have implemented a software application called MoldATRIX. This software generates useful statistics and displays critical information about the cell colony area. Our results were obtained by analyzing a series of digital images of Aspergillus niger cultures at different time intervals. Moreover, our results show the behavior of Aspergillus niger on leather.