The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small num...

The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determin...

The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike. The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and theoretical investigations. Here, we review recent theoretical progress by concentrating on quantum-chemical, molecular dynamics-based approaches to short DNA stra...

We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localization lengths (crudely speaking, the length over which electrons travel). Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations...

UNLABELLED RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary struct...

We developed a multithreaded parallel implementation of a sequence alignment algorithm that is able to align whole genomes with reliable output and reasonable cost. This paper presents a performance evaluation of the whole genome comparison tool called ATGC—Another Tool for Genome Comparison, on a Hyper-Threading multiprocessor. We use our application to determine the system scalability for thi...

This dissertation describes a comprehensive study of the Zγ → eeγ/μμγ/νν̄γ process. The data have been collected with the DØ detector at the Fermilab Tevatron pp̄ collider with the center-of-mass energy of 1.96 TeV, and correspond to up to 3.6 fb−1 of integrated luminosity. Firstly, in this study we perform a measurement of the Zγ production cross section. The measured cross sections in both ``γ ...