SAMBA: hardware accelerator for biological sequence comparison

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/.

[1]  Jean Vuillemin.  On Computing Power , 1994, Programming Languages and System Architectures.

[2]  Dominique Lavenier,et al.  Systolic filter for fast DNA similarity search , 1995, Proceedings The International Conference on Application Specific Array Processors.

[3]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[4]  Dzung T. Hoang,et al.  Searching genetic databases on Splash 2 , 1993, [1993] Proceedings IEEE Workshop on FPGAs for Custom Computing Machines.

[5]  Jean Sallantin,et al.  High Speed Pattern Matching in Genetic Data Base with Reconfigurable Hardware , 1994, ISMB.

[6]  D. Archambaud,et al.  Systolic Implementation of Smith and Waterman Algorithm on a SIMD Coprocessor , 1995 .

[7]  Richard Hughey,et al.  Kestrel: A Programmable Array for Sequence Analysis , 1996, Proceedings of International Conference on Application Specific Systems, Architectures and Processors: ASAP '96.

[8]  P Guerdoux-Jamet,et al.  Searching for a family of orphan sequences with SAMBA, a parallel hardware dedicated to biological applications. , 1996, Biochimie.

[9]  Mary Jane Irwin,et al.  A SIMD solution to the sequence comparison problem on the MGAP , 1994, Proceedings of IEEE International Conference on Application Specific Array Processors (ASSAP'94).

[10]  Michael S. Waterman,et al.  Biological information signal processor , 1991, Proceedings of the International Conference on Application Specific Array Processors.

[11]  O. Gotoh.  An improved algorithm for matching biological sequences. , 1982, Journal of molecular biology.

[12]  R.K. Singh,et al.  BioSCAN: a VLSI-based system for biosequence analysis , 1991, [1991 Proceedings] IEEE International Conference on Computer Design: VLSI in Computers and Processors.

[13]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[14]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[15]  W. Pearson.  Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. , 1991, Genomics.

[16]  Andrzej Wozniak,et al.  Using video-oriented instructions to speed up sequence comparison , 1997, Comput. Appl. Biosci..