Open Access. Powered by Scholars. Published by Universities.®

Biochemistry, Biophysics, and Structural Biology Commons

Open Access. Powered by Scholars. Published by Universities.®

Retrospective Theses and Dissertations

2006

Biostatistics

Articles 1 - 2 of 2

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

A Modular Data Analysis Pipeline For The Discovery Of Novel Rna Motifs , Justin Schonfeld Jan 2006

A Modular Data Analysis Pipeline For The Discovery Of Novel Rna Motifs , Justin Schonfeld

Retrospective Theses and Dissertations

This dissertation presents a modular software pipeline that searches collections of RNA sequences for novel RNA motifs. In this case the motifs incorporate elements of primary and secondary structure. The motif search pipeline breaks up sets of RNA sequences into shortened segments of RNA primary sequence. The shortened segments are then folded to obtain low energy secondary structures. The distance estimation module of the pipeline then calculates distances between the folded bricks, and then analyzes the resulting distance matrices for patterns;An initial implementation of the pipeline is applied to synthetic and biological data sets. This implementation introduces a new ...


Bayesian Recombination Detection Modeling And Application, Fang Fang Jan 2006

Bayesian Recombination Detection Modeling And Application, Fang Fang

Retrospective Theses and Dissertations

As a key evolutionary process, recombination shapes the genetic structure of virus populations. The increased availability of virus sequences provides a chance to study virus recombination through molecular data. Many statistical methods have been developed, and a lot of the methods are phylogenetic-based. My research focuses on recombination modeling and data analysis;I first apply an existing phylogenetic-base method, Bayesian dual change-point model (DMCP), to investigate the role of representative data types for recombination study. We conclude that consensus sequences are an all-around robust representative of virus genotypes. Using consensus data we study recombination of all full-length hepatitis B virus ...