SEI(BIO): DNA Inverted Repeats: Sensitive Detection Methods and Research Database

SEI(BIO)：DNA 反向重复：灵敏检测方法和研究数据库

• 批准号: 0612153
• 负责人: Gary Benson
• 金额: $ 66.9万
• 依托单位: Trustees of Boston University
• 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: 2006-07-01 至 2010-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0612153&HistoricalAwards=false
• 关键词: SEI; BIO; DNA; Inverted; Repeats

An inverted repeat (IR) consists of two copies of homologous DNA separated by a spacer region, with one copy inverted and complemented relative to the other. IRs occur frequently in genomic DNA and can have profound effects on chromosomal function and gene expression. IRs are a common component of RNA secondary structure, and are known to contribute to RNA interference and micro-RNA formation. A lack of sensitive, comprehensive, and efficient detection programs and databases has hampered the identification, annotation, and the study of IR functions. This project will explore and test new, efficient algorithmic methods for detecting approximate and exact IRs in genomic length sequences and create new data sets on the occurrence and characteristics of IRs in many genomes. It has three major goals: 1) To develop an Inverted Repeats Finder (IRF) program to detect approximate and exact IRs in long genomic sequences. 2) To develop a web-accessible, user-friendly, Inverted Repeats Database (IRDB) which will contain comprehensive information on IRs occurring in publicly available genomes. 3) To conduct collaborative research studies using IRF. The first study will examine the occurrence of cruciform structures in the human and other genomes in order to identify IR characteristics that make cruciform extrusion likely. The second study will examine the relationships, in mitochondrial DNA, among short imperfect repeats, age related deletions, and species life span.The IRF/IRDB software and data sets they produce will directly enhance the broader infrastructure for research in genome biology, genome evolution, chromosome architecture, and comparative genomics. This project will provide opportunities in research to graduate, undergraduate and high school students in the PI's lab, including participation by members of underrepresented groups, and it will include outreach to high school mathematics and biology teachers through curriculum development in interdisciplinary topics in computational biology and bioinformatics. As with other resources previously developed by the PI, all computer tools resulting from this project will be freely available to the research community through a high capacity website maintained in the PI's lab.

反向重复序列（IR）由两个拷贝的同源DNA组成，它们被间隔区隔开，其中一个拷贝相对于另一个拷贝反向并互补。IR经常出现在基因组DNA中，并对染色体功能和基因表达产生深远影响。 IR是RNA二级结构的常见组分，并且已知有助于RNA干扰和micro-RNA形成。缺乏灵敏、全面、高效的检测程序和数据库，阻碍了红外光谱功能的识别、注释和研究。该项目将探索和测试新的，有效的算法方法，用于检测基因组长度序列中的近似和精确IR，并创建关于许多基因组中IR的发生和特征的新数据集。 它有三个主要目标：1）开发一个反向重复序列（IRF）程序来检测长基因组序列中的近似和精确IR。2)开发一个可通过网络访问、用户友好的反向重复数据库（IRDB），其中将包含有关公开基因组中发生的IR的全面信息。 3)利用综合资源框架进行合作研究。 第一项研究将检查十字形结构在人类和其他基因组中的出现，以确定使十字形挤出可能的IR特征。 第二项研究将研究线粒体DNA中的短不完美重复序列、年龄相关缺失和物种寿命之间的关系，IRF/IRDB软件和数据集将直接增强基因组生物学、基因组进化、染色体结构和比较基因组学研究的更广泛基础设施。 该项目将为PI实验室的研究生，本科生和高中生提供研究机会，包括代表性不足的群体成员的参与，并将包括通过计算生物学和生物信息学跨学科主题的课程开发与高中数学和生物学教师的联系。 与PI以前开发的其他资源一样，该项目产生的所有计算机工具将通过PI实验室维护的高容量网站免费提供给研究界。