Multi-Purpose Parallel Process for Biosequence Analysis

生物序列分析的多用途并行处理

• 批准号: 9423985
• 负责人: Richard Hughey
• 金额: $ 55.73万
• 依托单位: University of California-Santa Cruz
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 1995
• 资助国家: 美国
• 起止时间: 1995-06-01 至 1999-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9423985&HistoricalAwards=false
• 关键词: Multi; Purpose; Parallel; Process; Biosequence

This project is building an application-specific computer system for biosequence comparison. The architecture is suitable for a wide range of sequence comparison methods, including the Smith- Waterman algorithm, BLAST, profile searches and dictionary methods. In addition, the architecture is being integrated with software for the statistical analysis of sequences using techniques such as hidden Markov models. The core of the architecture is a linear array of SIMD processing elements, each with a small local memory. A single chip can contain 64 of these elements, so a board with 20 chips will hold 1280 processors. The processing elements have been tuned to sequence comparison by incorporating a single cycle add-and-min instruction and a data-path for quickly recording the results of the instruction. Software, I/O, and algorithms have been considered in the design of this architecture; the resulting balanced implementation should result in high performance at low cost.

本项目正在建立一个用于生物序列比较的专用计算机系统。 该体系结构适用于广泛的序列比较方法，包括Smith-Waterman算法、BLAST、概况搜索和字典方法。 此外，该架构正在与使用隐马尔可夫模型等技术进行序列统计分析的软件相结合。 该架构的核心是一个线性阵列的SIMD处理元件，每个具有一个小的本地存储器。 一个芯片可以包含64个这样的元件，所以一个有20个芯片的电路板可以容纳1280个处理器。 处理元件已经被调整为通过合并单个周期加-减指令和用于快速记录指令结果的数据路径来进行序列比较。 软件，I/O和算法已被认为是在这个架构的设计，由此产生的平衡实施应导致高性能，低成本。