SAMBA: Hardware Accelerator for Biologucal Sequence Comparison

Pascale Guerdoux-Jamet - Dominique LAVENIER

CABIOS, to be published, 1997

Abstract

Motivations: SAMBA is a 128 processor hardware accelerator for speeding up the sequence comparison process. 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 among other existing systems and highlights the original features.

Results: Real performance obtained from the prototype is shown. For example, a sequence of 300 amino acids is scanned against SWISS-PROT-34 (21210389 residues) in 30 seconds using the Smith and Waterman algorithm. More time consuming applications, like the bank to bank comparison, are performed in a few hours instead of days of computation on standard workstations. Today technology allows the prototype to fit onto a single PCI board for plugging into any PC or workstation.