DNA Sequence Evolution with Neighbor-Dependent Mutation

DNA Sequen e Evolution with Neighbor-Dependent Mutation

DNA Sequence Fragment Containing C to A Mutation as a Convenient Mutation Standard for DHPLC Analysis

Objective(s):  Denaturing high performance liquid chromatography (DHPLC) is a high throughput approach for screening DNA sequence variations. To assess oven calibration, cartridge performance, buffer composition and stability, the WAVE Low and High Range Mutation Standards are employed to ensure reproducibility and accuracy of the chromatographic analysis. The purpose of this study was to provi...

A Markov Chain Monte Carlo Expectation Maximization Algorithm for Statistical Analysis of DNA Sequence Evolution with Neighbor-Dependent Substitution Rates

The evolution of DNA sequences can be described by discrete state continuous time Markov processes on a phylogenetic tree. We consider neighbor-dependent evolutionary models where the instantaneous rate of substitution at a site depends on the states of the neighboring sites. Neighbor-dependent substitution models are analytically intractable and must be analyzed using either approximate or sim...

Nucleotide sequence preservation of human mitochondrial DNA ( mutation / evolution / recombinant DNA / DNA

Recombinant DNA techniques have been used to quantitate the amount of nucleotide sequence divergence in the mitochondrial DNA population of individual normal humans. Mitochondrial DNA was isolated from the peripheral blood lymphocytes of five normal humans and cloned in M13 mphl; 49 kilobases of nucleotide sequence information was obtained from 248 independently isolated clones from the five no...

Sequence Dependent Elasticity of DNA

The DNA contained in every living cell not only stores the genetic information; it functions in a complex molecular network that can condense, transcribe, replicate and repair genes. The essential role played by the sequence dependent structure and deformability of DNA in these basic processes of life, has received increasing attention over the past years. The present work aims at better unders...