LIKELIHOOD OF SEQUENCES WITH RECOMBINATION AND SELECTION

重组和选择序列的可能性

• 批准号: 2190723
• 负责人: Joseph Felsenstein
• 金额: $ 13.81万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 1995
• 资助国家: 美国
• 起止时间: 1995-01-01 至 1998-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2190723
• 关键词: biochemical evolution; computer assisted sequence analysis; computer program /software; genetic models; genetic recombination; genetic techniques; mathematical model; method development; model design /development; natural selections; nucleic acid sequence; population genetics; statistics /biometry

DESCRIPTION: Dr. Joseph Felsenstein of the University of Washington proposes a 5-year study of methods for constructing likelihoods of DNA sequences under the influence of recombination and selection. This new work builds on his previous likelihood evaluations for phylogenetic trees. Dr. Felsenstein's specific objective is to develop methods for analyzing data from several sequences of the same region from a single population with the special interest being to extend ML methods to accommodate recombination among sites. These methods will allow inferences to be made about the patterns of natural selection at specific sites, and will allow estimation of population parameters such as population size or migration rate. The feature of consideration of recombination between adjacent nucleotide sites will be allowed as a means of adding to the realism of the analyses. Although the method of maximum likelihood offers the best statistical framework on which to base inferences from data, there are considerable computational difficulties in evaluating likelihood functions. The problem is that sums must be taken over all possible gene trees linking any sample of sequences. Recombination increases this number. Modern computing methods, including applications of the Metropolis algorithm, allow progress to be made by sampling some of the possible trees in a way that depends on their contribution to the overall likelihood. The necessary computer programs are time-consuming to construct and check, and Dr. Felsenstein will make them available without charge over the Internet. He has previously made available his phylogeny construction package PHYLIP.

描述：华盛顿大学的约瑟夫·费尔森斯坦博士 提出了一项为期5年的构建DNA可能性方法的研究 在重组和选择的影响下序列。 这个新 工作是基于他以前的系统发育评估 树木。 费尔森斯坦博士的具体目标是开发分析的方法 来自同一区域的几个序列的数据 特别的兴趣是扩展ML方法以适应 站点之间的重组。 这些方法将允许推论是 关于特定站点的自然选择模式的制作，并将 允许估计人口参数，例如人口规模或 迁移率。 考虑重组的特征 将允许相邻的核苷酸位点作为增加 分析的现实主义。 尽管最大似然的方法提供了最佳的统计 从数据中推断出的框架，有很多 评估似然函数的计算困难。 这 问题是必须在所有可能的基因树上获取总和 任何序列样本。 重组增加了这个数字。 现代的 计算方法，包括大都市算法的应用， 通过抽样某些可能的树木来取得进展 取决于它们对整体可能性的贡献。 这 必要的计算机程序耗时构建和检查， Felsenstein博士将无需负责 互联网。 他以前已经提供了他的系统发育结构 包装门。