Reliable Assembler for Whole Genome Shotgun Data.

全基因组霰弹枪数据的可靠组装器。

• 批准号: 6789377
• 负责人: JAMES A YORKE
• 金额: $ 17.48万
• 依托单位: UNIV OF MARYLAND, COLLEGE PARK
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-08-13 至 2006-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6789377
• 关键词: computer assisted sequence analysis; computer program /software; computer system design /evaluation; gene duplication; genetic mapping; genetic polymorphism; genetic screening; genome; molecular biology information system; nucleic acid repetitive sequence

DESCRIPTION (provided by applicant): Our main goal is to create a whole genome shotgun assembler for large repetitive genomes, that is superior at finding the sequence in repeat regions. Our most obvious departure from previous methods is the use of mated pairs in the beginning of the assembly, and to begin by building what we call a "'virtual physical map," that determines the relative positions of BACs in the genome. For our assembly we will only require whole genome shotgun sequence data, including BAC end reads. There are several tasks that we propose to accomplish. * To develop an integrated code that performs the assembly and outputs the consensus sequence along with quality values. We intend to document our code and post the source on the Internet to make it available to the scientific community around the world. * To make our program modular so that groups (such as the group at Baylor) can use parts of our assembler separately, including the overlapper routine and virtual physical map routine. * To evaluate the reliability of our assembler using data from a finished genome such as C. elegans. * To compare the performance of our assembler to other existing assemblers such as ARACHNE and Phusion using publicly available read data for human and mosquito genomes. * To assemble the mouse and rat genomes using publicly available read data and compare our (draft) assembly with publicly available draft assemblies. The results of our investigations will be published in peer-reviewed scientific journals. We are purely academic, not-for profit research group and we do not plan to patent or in any other way restrict the community's access to our software and results. Our research is directed toward uncovering more of the sequence than existing whole genome shotgun assemblers can provide, in highly repetitive genomes, like human or mouse. Our approach may find more genes and lead to better understanding of the genetic structure of the species. The ultimate goal of this work is of course the public health benefits expected from more accurately determining and better understanding the human genome.

描述（由申请人提供）： 我们的主要目标是为大重复基因组创建一个整个基因组shot弹枪汇编器，这在重复区域中找到了序列。我们与以前的方法最明显的不同是在组装开始时使用配对对，并首先要构建我们称为“虚拟物理图”的内容，该映射确定了BAC在基因组中的相对位置。对于我们的组装，我们只需要全基因组shot弹枪序列数据，包括BAC末端读数。 我们建议完成几个任务。 *开发一个集成的代码，该代码执行组装并输出共识序列以及质量值。我们打算记录我们的代码并将其发布在互联网上，以使其可以向世界各地的科学界使用。 *为了使我们的程序模块化，以便组（例如贝勒的组）可以单独使用我们的汇编程序的一部分，包括重叠的例程和虚拟物理地图例程。 *使用成品基因组（例如秀丽隐杆线虫）的数据评估汇编程序的可靠性。 *使用人类和蚊子基因组公开可用的读取数据将我们的组装商的性能与其他现有汇编者（例如Arachne和Phusion）进行比较。 *使用公开可用的读取数据组装鼠标和大鼠基因组，并将我们的（草稿）组件与公共可用的草稿组件进行比较。 我们的调查结果将在经过同行评审的科学期刊上发表。我们纯粹是学术，非利润研究小组，我们不打算专利或以任何其他方式限制社区对我们的软件和结果的访问。 我们的研究是针对揭示比现有的整个基因组shot弹枪汇编者可以在高度重复的基因组（如人类或小鼠）中提供的序列更多的。我们的方法可能会发现更多基因，并可以更好地理解该物种的遗传结构。这项工作的最终目标当然是更准确地确定和更好地理解人类基因组所期望的公共卫生益处。