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 (21 210 389 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. AVAILABILITY: SAMBA can be tested on the WEB server at URL http://www.irisa.fr/SAMBA/.

This paper presents a systolic filter for speeding up the scan of DNA databases. The filter acts as a co-processor which performs the more intensive computations occurring during the process. Our validation, based on a FPGA prototype board tightly connected to a workstation, has shown that the filter may boost the performance of the machine by a factor ranging from 50 to 400 over current workstations.