UTILIZATION OF SPECIALIZED HARDWARE FOR DNA SEQUENCE ANALYSIS

利用专用硬件进行 DNA 序列分析

• 批准号: 3774984
• 负责人: J I POWELL
• 金额: --
• 依托单位: CENTER FOR INFORMATION TECHNOLOGY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/3774984
• 关键词: DNA; computer assisted sequence analysis; computer system design /evaluation; computer system hardware

An ABI inherit system was purchased by DCRT and is being made available as a shared resource to NIH intramural scientists. Scientists purchase Macintosh client software from ABI and access the Inherit system over the NIH network. Inherit makes heavy use of specialized hardware, the Fast Data Finder (FDF), a parallel processor capable of scanning and comparing over 15 million characters per second. This system is primarily designed for: (1) assembly of medium to large sequencing projects; (2) searching the gene and protein databases for homologous gene sequences; and (3) searching quickly for genetic motifs such as regulatory elements. A pattern search language incorporated in the system allows for very complicated query formulations. DCRT is pursuing discussions with ABI on a cooperative agreement to allow DCRT access to source code to port Server software to additional UNIX platforms, including the NIH Convex. In connection with the ABI Inherit evaluation, a critical, quantitative comparison was done of several different commercial computer programs designed for sequence assembly and analysis. The purpose of this study was two fold: (1) to gain experience and expertise in the use of several different sequence assembly programs; and (2) to evaluate these programs as to their speed and accuracy in assembly and in their ease of use. Six sequence assembly packages have been examined. To evaluate the speed and quality of sequence assembly, the rat multidrug resistant gene (RATMDRM, 5,254 base pairs) sequence was randomly split into 58 overlapping fragments, each 200-400 basepairs in length. From 0 to 15% error was randomly added to these fragments based on the distribution of error found in the original fragments that were used to find the assembly.

DCRT购买了一个ABI继承系统，并正在提供 作为NIH内部科学家的共享资源。 科学家购买 来自ABI的Macintosh客户端软件并通过访问继承系统 NIH网络。 Inherit大量使用专用硬件， 数据并行处理器（FDF），能够扫描和比较 每秒超过1500万个字符 该系统主要设计 用于：（1）组装中型到大型测序项目;（2）搜索 同源基因序列的基因和蛋白质数据库;以及（3） 快速搜索基因基序，如调节元件。 一 结合在系统中的模式搜索语言允许非常 复杂的查询公式。 DCRT正在与ABI进行讨论 在一个合作协议，允许DCRT访问源代码的端口 服务器软件到其他UNIX平台，包括NIH Convex。 结合ABI Inherit评估， 比较了几种不同的商业计算机程序 用于序列组装和分析。 本研究的目的 （1）获得使用几种方法的经验和专业知识; 不同的序列组装程序;和（2）评估这些程序 它们在组装中的速度和精度以及它们的易用性。 六 序列组装包已被检查。 为了评估速度和 序列组装的质量，大鼠多药耐药基因（RATMDRM， 5，254个碱基对）序列随机分成58个重叠的 片段，每个片段长度为200-400个碱基对。 从0到15%的误差是 随机添加到这些片段的基础上分布的错误 在用来寻找装配体的原始片段中找到的。