Bioinformatics analysis of large-scale viral sequences

Large Scale Experiments Data Analysis for Estimation of Hydrodynamic Force Coefficients Part 1: Time Domain Analysis

This paper describes various time-domain methods useful for analyzing the experimental data obtained from a circular cylinder force in terms of both wave and current for estimation of the drag and inertia coefficients applicable to the Morison’s equation. An additional approach, weighted least squares method is also introduced. A set of data obtained from experiments on heavily roughened circul...

Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences

The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomic sequences. Combining discrete direct and double Fourier transforms, we studi...

Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology

Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identifi...

Viral Genomics and Bioinformatics

A stochastic analysis of three viral sequences.

This paper analyzes the nucleotide sequences of three viruses: Kunjin, west Nile, and yellow fever. Each virus has one long open reading frame of greater than 10,200 nucleotides that codes for four structural and seven nonstructural genes. The Kunjin and west Nile viruses are the most closely related pair, when assessed on the basis of matches between their nucleotide sequences. As would be exp...