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A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
The characterization of the long-range order and fractal properties of DNA sequences has proved a difficult though highly rewarding task due mainly to the mosaic character of DNA consisting of many interwoven patches of various lengths with…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
We introduce a simple model for DNA evolution. Using the method of Peng et al.$^1$, we investigate the fractal properties of the system. For small chains and chains of intermediate size we find a fractal exponent that indicates the…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
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)…
A number of signal processing and statistical methods can be used in analyzing either pieces of text or DNA sequences. These techniques can be used in a number of ways, such as determining authorship of documents, finding genes in DNA, and…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
This paper examines two methods for finding whether long-range correlations exist in DNA: a fractal measure and a mutual information technique. We evaluate the performance and implications of these methods in detail. In particular we…
We study statistical properties of DNA chains of thirteen microbial complete genomes. We find that the power spectrum of several of the sequences studied flattens off in the low frequency limit. This implies that the correlation length in…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…