RUI: Detection and Analysis of Fused Genes in Eukaryotic Genomes.

RUI：真核基因组中融合基因的检测和分析。

• 批准号: 0920697
• 负责人: Andre Cavalcanti
• 金额: $ 21.14万
• 依托单位: Pomona College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2012-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0920697&HistoricalAwards=false
• 关键词: RUI; Detection; Analysis; Fused; Genes

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).Fusion genes are important markers of evolution and can also aid in identifying protein function and protein interactions. Despite their importance and potential applications in research, few studies focused on identifying and characterizing fusion genes in eukaryotic species. One objective of this project is to perform a survey of sequenced eukaryotic genomes to identify and characterize fusion genes. In order to achieve this goal, two software programs will be developed. Gene Fuser/Defuser will allow users to detect evolutionarily fused genes in eukaryotic genomes and EukGenomeBlast will allow researchers to determine the phylogenetic distribution of fusion genes and metabolic pathways among a phylogenetically diverse set of complete eukaryotic genomes. In addition, Gene Fuser/Defuser can be used to detect faulty gene predictions in genome projects. Several of the genes detected by the program are not truly fused, but are instead the result of faulty gene predictions. Detection of these faulty gene models makes Gene Fuser/Defuser a useful tool for the correction of genome annotation.BROADER IMPACTS:Both programs will be available online and will be easy to use even for non-specialists. EukGenomeBlast, in particular, has applications that will allow researchers with no programming experience to perform more detailed and focused BLAST searches using their genes or group of genes of interest. Another important factor in the design of these programs is their suitability for use in an undergraduate classroom setting. Many colleges do not have the resources to hire full-time bioinformaticians and many bioinformatics tools are complex and difficult to use making it a challenge for a non-specialist to incorporate them into undergraduate courses. This project will create simple modules, with detailed protocols and tutorials, that can be used in undergraduate courses as an introduction to genomic and bioinformatics research. The programs are also ideally suited for undergraduate research as they generate smaller research projects that can be undertaken by undergraduate students. Each fusion gene identified can become its own project, allowing a student or a small group of students to perform a complete analysis of a given fusion gene in a semester.

该奖项是根据2009年美国复苏和再投资法案（公法111-5）资助的。融合基因是进化的重要标志，也可以帮助鉴定蛋白质功能和蛋白质相互作用。尽管融合基因在研究中的重要性和潜在应用，但很少有研究关注真核生物物种中融合基因的鉴定和表征。该项目的目的之一是执行一个调查测序真核生物基因组，以鉴定和表征融合基因。为了实现这一目标，将开发两个软件程序。Gene Fuser/Defuser将允许用户检测真核生物基因组中的进化融合基因，EukGenomeBlast将允许研究人员确定融合基因的系统发育分布和系统发育多样化的完整真核生物基因组中的代谢途径。此外，基因Fuser/Defuser可用于检测基因组计划中错误的基因预测。该程序检测到的一些基因并没有真正融合，而是错误的基因预测的结果。这些错误基因模型的检测使基因融合/去融合成为校正基因组注释的有用工具。更广泛的影响：这两个项目都将在网上提供，即使对非专业人士也很容易使用。特别是EukGenomeBlast，它的应用程序允许没有编程经验的研究人员使用他们的基因或感兴趣的基因组进行更详细、更集中的BLAST搜索。设计这些课程的另一个重要因素是它们是否适合在本科课堂环境中使用。许多大学没有足够的资源聘请全职生物信息学家，而且许多生物信息学工具复杂且难以使用，对于非专业人士来说，将它们纳入本科课程是一项挑战。该项目将创建简单的模块，带有详细的协议和教程，可用于本科课程，作为基因组和生物信息学研究的入门。这些项目也非常适合本科生的研究，因为它们可以产生较小的研究项目，可以由本科生承担。每个确定的融合基因都可以成为自己的项目，允许一个学生或一小群学生在一个学期内对给定的融合基因进行完整的分析。