Samba: Hardware accelerator for biological sequence comparison

Abstract

Motivation: 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. Results: Real performance obtained from the prototype is demonstrated. For example, a sequence of 300 amino acids is scanned against SWISS-PROT-34 (21 210389 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 tofit onto a single PCI board for plugging into any PC or workstation. Availability: SAMBA can he tested on the WEB server at URL http://www.irisa.fr/SAMBA/ Contact: E-mail: lavenier@irisa.fr. © 1997, Oxford University Press.