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

一个反向重复序列（IR）由同源DNA的两个拷贝组成，由间隔区隔开，其中一个拷贝相对于另一个拷贝反转和互补。IRs经常发生在基因组DNA中，对染色体功能和基因表达有深远的影响。IRs是RNA二级结构的常见组成部分，已知有助于RNA干扰和微RNA的形成。缺乏敏感、全面、高效的检测程序和数据库阻碍了红外功能的识别、标注和研究。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近似和精确的IRs，并创建关于许多基因组中IRs的发生和特征的新数据集。它有三个主要目标：1)开发一个倒置重复序列查找器（IRF）程序来检测长基因组序列中的近似和精确的IRs。2)开发一个可访问网络的、用户友好的反向重复序列数据库（IRDB），该数据库将包含在公开可用的基因组中发生的反向重复序列的全面信息。3)利用IRF开展合作研究。第一项研究将检查人类和其他基因组中十字形结构的发生，以确定使十字形挤压可能发生的IR特征。第二项研究将检查线粒体DNA中短的不完美重复、与年龄相关的缺失和物种寿命之间的关系。他们生产的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的基础设施。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，并将通过计算生物学和生物信息学跨学科主题的课程开发向高中数学和生物教师提供服务。与PI先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社区。

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.