Extending Bayesian Phylogenetic Analysis

描述（由申请人提供）：对于细菌基因组的基因组分析，水平基因转移是一个复杂因素，导致不同基因具有不一致的历史。我计划在这种水平基因转移的情况下开发估计细菌物种系统发育的方法。我还将开发一些方法，通过将具有相似进化参数实现值的基因分组在一起，使生物学家能够发现数据中的模式。最后，我将开发更现实的蛋白质进化模型，利用最尖端的工作来从头开始预测蛋白质结构。使用相同的统计框架，我将尝试通过结合吉布自由能信息和比较序列信息来预测RNA二级结构。

DESCRIPTION (provided by applicant): For genomic analyses of bacterial genomes, horizontal gene transfer is a complicating factor, causing different genes to have discordant histories. I plan to develop methods for estimating bacterial species phylogeny in the face of this horizontal gene transfer. I will also develop methods that allow the biologist to uncover patterns in the data, by grouping together genes that have similar realized values of evolutionary parameters. Finally, I will develop more realistic models of protein evolution that take advantage of the most cutting-edge work for the ab initio prediction of protein structure. Using the same statistical framework, I will attempt to predict RNA secondary structure by combining information on the Gibb's free energy with comparative sequence information. The methods developed in the course of this research will be implemented in the next generation of the MrBayes software. 1 PUBLIC HEALTH RELEVANCE: The comparison of DNA sequences from different organisms allows scientists to learn about the processes that shape genomes. For example, by comparing the DNA sequences of deferent genes, we can learn about how natural selection has acted. This proposal develops improved methods for the analysis of DNA sequences. 1