A hybrid architecture for bioinformatics

被引：8

作者：

Schmidt, B

Schröder, H

Schimmler, M

机构：

[1] Nanyang Technol Univ, Sch Comp Engn, Singapore 639798, Singapore

[2] Tech Univ Braunschweig, Inst Datentech & Kommunikationsnetze, D-38106 Braunschweig, Germany

来源：

FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE | 2002年 / 18卷 / 06期

关键词：

hybrid parallel architecture; high performance biosequence database searching; Smith-Waterman algorithm; instruction systolic array; cluster computing;

D O I：

10.1016/S0167-739X(02)00058-4

中图分类号：

TP301 [理论、方法];

学科分类号：

081202 ;

摘要：

We present a hybrid parallel system based on commodity components to gain supercomputer power at low cost. The architecture is built around a coarse-grained PC-cluster linked by a high-speed network and fine-grained parallel processor arrays connected to each node. Identifying applications that profit from this kind of processing power is critical to justify the use of such a system. In this paper, we present a new approach to high performance protein database scanning with hybrid computing. To derive an efficient mapping onto this architecture, we designed an instruction systolic sequence comparison algorithm. This results in a database scanning implementation with significant runtime savings. (C) 2002 Elsevier Science B.V. All rights reserved.

引用

页码：855 / 862

页数：8

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