Design and implementation of a parallel architecture for biological sequence comparison
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.
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