A study on the correlation of nucleotide skews and the positioning of the origin of replication: different modes of replication in bacterial species

Deviations from Chargaff's 2nd parity rule, according to which A∼T and G∼C in single stranded DNA, have been associated with replication as well as with transcription in prokaryotes. Based on observations regarding mainly the transcription-replication co-linearity in a large number of prokaryotic species, we formulate the hypothesis that the replication procedure may follow different modes between genomes throughout which the skews clearly follow different patterns. We draw the conclusion that multiple functional sites of origin of replication may exist in the genomes of most archaea and in some exceptional cases of eubacteria, while in the majority of eubacteria, replication occurs through a single fixed origin

Optimal Computation of Overabundant Words

The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word w in a given sequence x can be used for classifying w as avoided or overabundant. The definitions used for the expectation and deviation of w in this statistical model were described and biologically justified by Brendel et al. (J Biomol Struct Dyn 1986). We have very recently introduced a time-optimal algorithm for computing all avoided words of a given sequence over an integer alphabet (Algorithms Mol Biol 2017). In this article, we extend this study by presenting an O(n)-time and O(n)-space algorithm for computing all overabundant words in a sequence x of length n over an integer alphabet. Our main result is based on a new non-trivial combinatorial property of the suffix tree T of x: the number of distinct factors of x whose longest infix is the label of an explicit node of T is no more than 3n-4. We further show that the presented algorithm is time-optimal by proving that O(n) is a tight upper bound for the number of overabundant words. Finally, we present experimental results, using both synthetic and real data, which justify the effectiveness and efficiency of our approach in practical terms

Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers

Scarce work has been done in the analysis of the composition of conserved non-coding elements (CNEs) that are identified by comparisons of two or more genomes and are found to exist in all metazoan genomes. Here we present the analysis of CNEs with a methodology that takes into account word occurrence at various lengths scales in the form of feature vector representation and rule based classifiers. We implement our approach on both protein-coding exons and CNEs, originating from human, insect (Drosophila melanogaster) and worm (Caenorhabditis elegans) genomes, that are either identified in the present study or obtained from the literature. Alignment free feature vector representation of sequences combined with rule-based classification methods leads to successful classification of the different CNEs classes. Biologically meaningful results are derived by comparison with the genomic signatures approach, and classification rates for a variety of functional elements of the genomes along with surrogates are presented. (C) 2014 Elsevier Inc. All rights reserved

Numerical Study of Travelling Waves in a Reaction - Diffusion System: Response to a Spatio-Temporal Forcing

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Chiral Selection of Rotating Waves in a Reaction-Diffusion System: The Effect of a Circularly Polarized Electromagnetic Field

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Chiral pattern selection induced by a Fokker-Planck diffusion law

It is pointed out that in a reaction-diffusion system near a chiral symmetry-breaking instability, a weak drift term in the diffusion law can induce a systematic selection between macroscopic three-dimensional patterns of opposite chirality. When the cause of the drift term is an external field, the orientation of the field with respect to the system determines the final chiral choice. The possible appearance of a drift term in the diffusion law, arising from the intrinsic asymmetry of the underlying material is also considered. In a one-dimensional system with periodic boundary conditions it is shown that the drift term may account for systematic selection between waves rotating in opposite directions. © 1992, Taylor & Francis Group, LLC. All rights reserved.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Morphogenesis in an asymmetric medium

Some key experiments of artificial production of situs inversus viscerum are briefly reviewed and a two-step mechanism for the explanation of the systematic asymmetric visceral arrangement in vertebrates is proposed. A two-variable reaction-diffusion system displaying a symmetry-breaking bifurcation is considered, and it is demonstrated that a slight asymmetry of the boundary conditions can give rise to a marked asymmetry in the resulting dissipative structure in both one-and three-dimensional systems. A criterion is formulated allowing classification of reaction-diffusion systems operating in a three-dimensional space with regard to their ability to incorporate slight asymmetries at the boundaries in the form of a chiral dissipative structure. © 1987 Society for Mathematical Biology.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

A Study of Fractality and Long-Range Order in the Distribution of Transposable Elements in Eukaryotic Genomes Using the Scaling Properties of Block Entropy and Box-Counting

Repeats or Transposable Elements (TEs) are highly repeated sequence stretches, present in virtually all eukaryotic genomes. We explore the distribution of representative TEs from all major classes in entire chromosomes across various organisms. We employ two complementary approaches, the scaling of block entropy and box-counting. Both converge to the conclusion that well-developed fractality is typical of small genomes while in large genomes it appears sporadically and in some cases is rudimentary. The human genome is particularly prone to develop this pattern, as TE chromosomal distributions therein are often highly clustered and inhomogeneous. Comparing with previous works, where occurrence of power-law-like size distributions in inter-repeat distances is studied, we conclude that fractality in entire chromosomes is a more stringent (thus less often encountered) condition. We have formulated a simple evolutionary scenario for the genomic dynamics of TEs, which may account for their fractal distribution in real genomes. The observed fractality and long-range properties of TE genomic distributions have probably contributed to the formation of the “fractal globule”, a model for the confined chromatin organization of the eukaryotic nucleus proposed on the basis of experimental evidence