Approximate Tandem Repeats Database

近似串联重复数据库

• 批准号: 0542751
• 负责人: Dina Sokol
• 金额: $ 32.13万
• 依托单位: CUNY Brooklyn College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-01 至 2010-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0542751&HistoricalAwards=false
• 关键词: Approximate; Tandem; Repeats; Database

City University New York, Brooklyn College receives an award to develop a tandem repeat database. Tandemly repeated DNA sequences are widespread throughout the human genome. They show suffcient variability among individuals in a population that they have become important in several fields. Researchers have been using tandem repeats in many areas including human identity testing (DNA fingerprinting), mapping studies, population studies, and gene prediction. This project creates a database containing an accounting of all tandem repeats within the human genome with bounded copy-to-copy differences. The steps include Design of an algorithm that finds all tandem repeats within a sequence; Implementing the algorithm in C++ or Java; Design of a website, and uploading the program as open-source code. The software will be run on the sequences of the human genome and stored in a database of results. At the end the results will be evaluated by comparing them to the repeats found using heuristic approaches.The proposed algorithm will be implemented by undergraduate students, satisfying the requirement each student has of completing a research project with a faculty member. Furthermore, the algorithm will be incorporated into a new undergraduate course on Computational Biology. Research results will be disseminated through major conferences and journal publications. A website will be created to enable others access to the source code and database.

纽约城市大学布鲁克林学院因开发串联重复数据库而获奖。串联重复的DNA序列广泛存在于整个人类基因组中。它们在种群中的个体之间表现出足够的变异性，因此在几个领域中变得很重要。研究人员已经在许多领域使用串联重复序列，包括人类身份测试（DNA指纹），作图研究，人口研究和基因预测。该项目创建了一个数据库，其中包含人类基因组中所有具有有限拷贝差异的串联重复序列。这些步骤包括设计一个算法，找到一个序列中的所有串联重复序列;在C++或Java中实现该算法;设计一个网站，并将程序作为开源代码上传。该软件将在人类基因组序列上运行，并存储在结果数据库中。最后，通过将结果与使用启发式方法发现的重复进行比较来评估该算法，该算法将由本科生实施，满足每个学生与教师一起完成研究项目的要求。此外，该算法将被纳入一个新的计算生物学本科课程。研究成果将通过主要会议和期刊出版物传播。将建立一个网站，使其他人能够访问源代码和数据库。