Algorithms and Software for Molecular Sequence Exploration

分子序列探索的算法和软件

• 批准号: 9723346
• 负责人: Daniel Gusfield
• 金额: $ 35.05万
• 依托单位: University of California-Davis
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 1997
• 资助国家: 美国
• 起止时间: 1997-09-01 至 2002-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9723346&HistoricalAwards=false
• 关键词: Algorithms; Software; Molecular; Sequence; Exploration

Comparison of bio-molecular sequences has become essential in modern molecular biology and biotechnology. This project will develop and test algorithmic techniques to explore DNA and protein sequences, with emphasis on techniques for newer or less analyzed biological phenomena. There are several areas of concentration: A fundamental re-examination of the biological basis for alignment models and parameters in light of the recently available sequence data and the accumulating understanding of mutation mechanisms; Expansion of parametric alignment methods to apply to a broader range of sequence analysis problems; Development of methods to organize a large set of alignments, in order to present alternative alignments without overwhelming the researcher; Formalizing notions of repeated substrings containing variations, and exploiting deep theorems from the study of exact repeats; Connecting the problem of protein structure alignment to a body of efficient techniques from Location Theory. Molecular sequence comparison is the essential complement of projects, such as the human genome project, that are obtaining the full DNA sequence transcript of various genomes. Comparison of sequences inside and across species has tremendously accelerated many tasks in molecular biology and biotechnology. The potential impact of this project will be in the development of more biologically based alignment models, in the production of novel software, and in the adaptation of mature mathematical and computational techniques to problems in molecular biology. Since sequence comparison has now become critical in molecular biology and in many aspects of commercial bio-technology and pharmaceutical companies, improved models and software for sequence comparison may have a significant impact on the way disease genes are identified, on the way newly identified genes are understood to function, and on the way new candidate molecular targets for medicines are identified. This work is funded by the Computational Biology Activity (BIO) and the program in the Theory of Computing (CISE).

在现代分子生物学和生物技术中，生物分子序列的比较已成为必不可少的。 该项目将开发和测试算法技术，以探索DNA和蛋白质序列，重点是新的或较少分析的生物现象的技术。 有几个集中的领域：根据最近可用的序列数据和对突变机制的不断积累的理解，对比对模型和参数的生物学基础进行基本的重新检查;扩展参数比对方法，以应用于更广泛的序列分析问题;开发组织大量比对的方法，以便在不压倒研究人员的情况下提出替代比对;形式化包含变化的重复子串的概念，并从精确重复的研究中探索深入的定理;将蛋白质结构比对问题与定位理论中的一系列有效技术联系起来。 分子序列比较是人类基因组计划等项目的必要补充，这些项目正在获得各种基因组的完整DNA序列转录本。 物种内部和跨物种的序列比较极大地加速了分子生物学和生物技术中的许多任务。 这个项目的潜在影响将是在开发更多的生物学为基础的比对模型，在生产新的软件，并在适应成熟的数学和计算技术的问题，在分子生物学。 由于序列比较在分子生物学中以及在商业生物技术和制药公司的许多方面已经变得至关重要，用于序列比较的改进的模型和软件可能对疾病基因的鉴定方式、对新鉴定的基因的功能的理解方式以及对药物的新候选分子靶标的鉴定方式具有显著影响。 这项工作由计算生物学活动（BIO）和计算理论（CISE）计划资助。