PARALLEL DNA SEQUENCE ASSEMBLY PROGRAM

描述(改编自《调查员摘要》)：调查员 将开发一种软件工具，用于组装在 大规模的猎枪测序项目。该软件将进行测试 第一个关于计算机从巨型数据库DNA序列中产生的DNA片段 然后是来自大规模测序项目的真实DNA片段。 该软件将免费分发给非营利组织。这个 调查员将协助将软件整合到测序中 基因组中心的环境。 这个项目的目标将通过两个主要方面来实现 对之前开发的DNA序列组装程序进行了改进。 第一个改进是制定解决问题的策略 由重复序列引起的。在这个策略中，所有的碎片 从重复序列中识别出，并且不确定 使用关于以下内容的附加信息来解析片段的组装 位于重复序列拷贝两侧的片段。 第二个改进是增加了组装的能力 通过在PVM中开发程序的并行版本来编写程序 本地计算机网络上的并行编程环境。这个 调查员将把最耗时的两部分 顺序程序，片段之间重叠的检测和 构建重叠群的片段比对。并行序列 汇编语言程序将能够使用许多计算能力 将数万个DNA片段组装成序列的计算机 误差率很低。调查员将改进多重序列 通过寻址读数帧移位来对准程序的比较 蛋白质、cDNA和基因组DNA序列。

DESCRIPTION (Adapted from the Investigator's Abstract): The investigator will develop a software tool for assembling DNA fragments generated in megabase- scale shotgun sequencing projects. The software will be tested first on DNA fragments generated by computers from megabase DNA sequences and then on real DNA fragments from large-scale sequencing projects. The software will be freely distributed to nonprofit organizations. The investigator will assist the integration of the software into sequencing environments at genome centers. The objective of this project will be achieved by making two major improvements to a DNA sequence assembly program developed previously. The first improvement is to develop a strategy for solving the problems caused by repetitive sequences. In this strategy, all the fragments from a repetitive sequence are identified, and the uncertainties in assembly of the fragments are resolved using additional information on the fragments that flank copies of the repetitive sequence. The second improvement is to increase the capacity of the assembly program by developing a parallel version of the program in the PVM parallel programming environment on a local network of computers. The investigator will parallelize the two most time-consuming parts of the sequential program, the detection of overlaps among fragments and the construction of fragment alignments for contigs. The parallel sequence assembly program will be able to use the computation power of many computers to assemble tens of thousands of DNA fragments into sequences of low error. The investigator will improve the multiple sequence alignment program by addressing reading frame shifts in comparison of protein, cDNA and genomic DNA sequences.