CAREER: New Technologies for Querying Pathway Databases

职业：查询路径数据库的新技术

• 批准号: 0845439
• 负责人: Tamer Kahveci
• 金额: $ 40万
• 依托单位: University of Florida
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-02-15 至 2015-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0845439&HistoricalAwards=false
• 关键词: CAREER; New; Technologies; Querying; Pathway

Unlike most bioinformatics data, such as DNA sequences and proteinstructures, pathways show the interactions of different bio-chemicalentities. Thus, each entity or subpathway can have a function in itspathway that the pathway can not realize without it. Formulating thesefunctions presents exciting computational challenges. This proposal develops algorithms for efficient and accuratecomputational analysis of pathways. The first step in achieving thisgoal is to build a mathematical model for functions of pathways andsubpathways. This proposal defines the function of a subpathway as itscontribution to the steady state of the entire pathway. Computing thiscontribution is a difficult problem especially for gene regulatorypathways. Existing methods can compute this for metabolic pathways,but they do not scale to even medium sized gene regulatorypathways. This proposal develops efficient methods for computingfunction.Finding the subpathway that has a desired function is a challengingproblem. There is no clear way of searching for subpathways withdesired functions using existing tools. This proposal developsefficient algorithms for searching subpathways with desired function.This proposal takes this one step further, and develops mathematicallysound algorithms for comparing two pathways so that the entities thatmap are functionally, homologically and topologically similar. Thisproposal also explores feature and reference-based index structuresfor biological pathway databases.Further information on the project can be found at the project webpage: http://bioinformatics.cise.ufl.edu/

与大多数生物信息学数据（如DNA序列和蛋白质结构）不同，途径显示了不同生物化学实体之间的相互作用。因此，每一个实体或子途径都可以在其途径中有一个功能，而没有它，途径就无法实现。制定这些功能提出了令人兴奋的计算挑战。该建议开发了有效和准确的计算分析的途径的算法。实现这一目标的第一步是建立通路和子通路功能的数学模型。这个建议将子途径的功能定义为它对整个途径稳定状态的贡献。计算这种贡献是一个困难的问题，特别是对基因调控途径。 现有的方法可以计算代谢途径，但它们甚至不能扩展到中等大小的基因调控途径。该方案为函数的计算提供了有效的方法，但寻找具有所需函数的子通路是一个具有挑战性的问题。使用现有的工具，没有明确的方法来搜索具有所需功能的子途径。这个建议发展了搜索具有所需功能的子路径的有效算法。这个建议更进一步，发展了比较两个路径的精确算法，使得映射的实体在功能上、同源性上和拓扑上相似。 该计划还探索了生物学途径数据库的特征和基于参考的索引结构。http://bioinformatics.cise.ufl.edu/