Reliable Assembler for Whole Genome Shotgun Data.

描述(由申请人提供)： 我们的主要目标是创建一个用于大型重复基因组的全基因组猎枪组装器，它在寻找重复区域的序列方面具有优势。我们与以前方法最明显的不同是在组装开始时使用配对，并从建立我们所说的“虚拟物理图谱”开始，它确定了BAC在基因组中的相对位置。对于我们的组装，我们只需要整个基因组猎枪序列数据，包括BAC末端读取。 我们建议完成几项任务。 *开发执行组装并输出共识序列和质量值的集成代码。我们打算将我们的代码记录下来，并将源代码发布在互联网上，以便向世界各地的科学界提供。 *使我们的程序模块化，以便组(如贝勒的组)可以单独使用我们的汇编程序的部分，包括重叠例程和虚拟物理映射例程。 *使用线虫等完成的基因组数据来评估我们组装器的可靠性。 *使用公开可用的人类和蚊子基因组读取数据，将我们的汇编器与其他现有汇编器(如Arachne和Phusion)的性能进行比较。 *使用公开可用的READ数据组装小鼠和大鼠基因组，并将我们的(草稿)组装与公开可用的草稿组装进行比较。 我们的调查结果将发表在同行评议的科学期刊上。我们是纯学术的、非营利性的研究团体，我们不打算申请专利或以任何其他方式限制社区访问我们的软件和结果。 我们的研究旨在揭示更多的序列，而不是现有的全基因组猎枪组装者在高度重复的基因组中所能提供的，比如人类或老鼠。我们的方法可能会发现更多的基因，并导致对物种遗传结构的更好理解。当然，这项工作的最终目标是通过更准确地确定和更好地了解人类基因组而预期的公共健康好处。

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.