III-CXT-Small: Graphs to Diversity: extracting genomic variation from sequence graphs

III-CXT-Small：多样性图表：从序列图中提取基因组变异

• 批准号: 0812111
• 负责人: Mihai Pop
• 金额: $ 44.54万
• 依托单位: University of Maryland, College Park
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-01 至 2013-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0812111&HistoricalAwards=false
• 关键词: III; CXT; Small; Graphs; Diversity

Recent advances in genome sequencing technologies have enabled thesequencing of bacteria directly from the environment, providing abroader outlook on the diversity of bacteria than ever beforepossible. Recent studies of environmental samples have revealedcomplex communities containing many previously unknown species, anduncovered a large amount of genetic variation and diversity even amongclosely related strains. Characterizing this genomic variation iscritical in studies of microbial ecology and evolution, yet currentlyavailable computational tools, originally developed for the study ofsingle organisms, are ill-suited for this task.This proposal aims to develop the theoretical and computationalinfrastructure for the study of genomic variation within mixtures oforganisms. The proposed research relies on both theoretical andempirical analyses of the structure of genome assembly graphs in orderto characterize graph signatures that are correlated with intra- andinter- species polymorphisms. A particular focus is placed onunderstanding and using the information provided by next generationsequencing technologies as well as other high-throughput experimentaltechniques. The proposed work provides critical analysis toolsto help biologists explore the genetic variation within theenvironment.Additional information about this project is available athttp://www.cbcb.umd.edu/research/Genomic_Variation.shtml.

基因组测序技术的最新进展使细菌能够直接从环境中测序，提供了比以往任何时候都更广阔的细菌多样性前景。最近对环境样本的研究揭示了包含许多以前未知的物种的复杂群落，并发现了大量的遗传变异和多样性，即使在密切相关的菌株之间也是如此。这种基因组变异的特征在微生物生态学和进化的研究中是至关重要的，但目前可用的计算工具，最初是为研究单个生物体而开发的，不适合于这项任务。提出的研究依赖于对基因组组装图结构的理论和经验分析，以表征与物种内和物种间多态相关的图形特征。特别关注理解和使用下一代测序技术以及其他高通量实验技术提供的信息。这项拟议的工作提供了关键的分析工具，帮助生物学家探索环境中的遗传变异。有关该项目的其他信息，请访问athttp://www.cbcb.umd.edu/research/Genomic_Variation.shtml.