Whole Genome Comparison on a Network of Workstations

Whole genome comparison consists of comparing or aligning genome sequences with a goal of finding similarities between them. Previously we have shown how SIMD extensions used in Intel processors can be used to efficiently implement the, genome comparing, Smith-Waterman algorithm. Here we present distributed version of that algorithm. We show that on somewhat outdated hardware we can achieve speeds upwards of 8000 MCUPS; one of the fastest implementations of the Smith-Waterman algorithm.