Design and Implementation of a Parallel Architecture
for Biological Sequence Comparison
P. Guerdoux-Jamet, D. Lavenier, C. Wagner, P.Quinton
EuroPar'96 Parallel Processing
Second International EuroPar Conference, Lyon, France, August 27-29
LNCS 1123, pp 11-24, aug 1996
Abstract
SAMBA is a full custom parallel hardware accelerator dedicated to the
comparison of biological sequences. It implements a parameterized
version of the Smith and Waterman algorithm allowing the computation
of local or global alignments with or without gap penalty. The
speed-up provided by SAMBA over standard workstations ranges from 50
to 500, depending on the application. SAMBA was designed with an
effort of less than one person/year. This includes the design,
fabrication and test of a full-custom VLSI chip which is used as a
building block for the 128 processor systolic array implementing the
string alignment algorithm. We describe the SAMBA architecture, its
performance characteristics, and we detail its design steps, from the
initial specification to its full implementation. We report a first
application of SAMBA to the study of yeast orphan sequences.
Postscript