Mathematical genomics

数学基因组学

• 批准号: 8867-2008
• 负责人: Sankoff, David
• 金额: $ 4.81万
• 依托单位: University of Ottawa
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2015
• 资助国家: 加拿大
• 起止时间: 2015-01-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=568625
• 关键词: Mathematical; genomics

We study the mathematics, statistics and computing of genome rearrangements, the evolutionary processes by which segments of chromosomes are inverted, moved around and exchanged. There is an algorithmic technology for inferring a minimizing sequence of operations necessary to transform one genome into another, where the operations are modeled on processes such as inversion, reciprocal translocation, chromosome fusion and fission, transposition of chromosomal segments. Once these inferences are made, however, there is a need for some way to statistically validate both the inferences and the assumptions of the evolutionary model. Our approach is to use models of random genomes to see to what extent there is an signal remaining in the comparative structure of the two genomes, or whether evolution has largely scrambled the order of each one with respect to the other. We work on the problem of the rearrangement median for three genomes as the basis for gene order phylogeny based on rearrangements, and apply it to chloroplast and mammalian data sets. We study the "genome halving problem" for ancient tetraploids and extensions to mixed ploidy gene order phylogenies. We apply this to the study of the "Saccharomyces complex" of yeast species. In comparing genomic maps, we introduce the notion of partially ordered genomes to take into account missing and unresolved data, and use this to compare the genomes of various cereal species. We also work on distinguishing mapping errors from genuine rearrangements of the genomes and we apply this to the comparison of the rice and sorghum genomes. We have defined a new measure of "generalized adjacency" as a useful tool in computing ancestral genomes within a phylogeny. This leads to many algorithmic and statistical questions we propose to investigate.

我们研究基因组重排的数学、统计学和计算，染色体片段倒转、移动和交换的进化过程。有一种算法技术，用于推断将一个基因组转化为另一个基因组所需的最小化操作序列，其中操作是基于诸如倒置，互惠易位，染色体融合和裂变，染色体片段转位等过程建模的。然而，一旦做出了这些推论，就需要某种方法来统计地验证这些推论和进化模型的假设。