Abstract
Comparison of biological (DNA or protein) sequences provides insight into molecular structure, function, and homology, and is increasingly important as the available databases become larger and more numerous. One method of increasing the speed of the calculations is to perform them in parallel. We present the results of initial investigations using the Intel iPSC/1 hypercube and the Connection Machine (CM-I) for these comparisons. Since these machines have very different architectures, the issues and performance trade-offs discussed have a wide applicability for the parallel processing of biological sequence comparisons.
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