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© Oxford University Press

SAMBA: hardware accelerator for biological sequence comparison

P. Guerdoux-Jamet 1 and D. Lavenier

IRISA, Campus de Beaulieu 35042 Rennes cedex, France

1To whom correspondence should be addressed

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{at}irisa.fr

Received on May 14, 1997; revised on July 9, 1997; accepted on July 18, 1997

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