Guerdoux-Jamet P, Lavenier D
IRISA, Rennes, France.
Comput Appl Biosci. 1997 Dec;13(6):609-15. doi: 10.1093/bioinformatics/13.6.609.
SAMBA (Systolic Accelerator for Molecular Biological Applications) is a 128 processor hardware accelerator for speeding up the sequence comparison process. The short-term objective is to provide a low-cost board to boost PC or workstation performance on this class of applications. This paper places SAMBA amongst other existing systems and highlights the original features.
Real performance obtained from the prototype is demonstrated. For example, a sequence of 300 amino acids is scanned against SWISS-PROT-34 (21 210 389 residues) in 30 s using the Smith and Waterman algorithm. More time-consuming applications, like the bank-to-bank comparison, are computed in a few hours instead of days on standard workstations. Technology allows the prototype to fit onto a single PCI board for plugging into any PC or workstation.
SAMBA can be tested on the WEB server at URL http://www.irisa.fr/SAMBA/.
SAMBA（用于分子生物学应用的收缩加速器）是一款拥有128个处理器的硬件加速器，用于加速序列比较过程。短期目标是提供一种低成本的板卡，以提升个人计算机或工作站在此类应用上的性能。本文将SAMBA与其他现有系统进行了比较，并突出了其独特特性。
展示了从原型机获得的实际性能。例如，使用史密斯-沃特曼算法，在30秒内就能将一段300个氨基酸的序列与SWISS-PROT-34（21210389个残基）进行比对。更耗时的应用，如库对库比较，在标准工作站上需要数天才能完成，而使用该原型机只需数小时。该技术使原型机能够适配到单个PCI板卡上，以便插入任何个人计算机或工作站。
