Parallel processing of biological sequence comparison algorithms

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. This research was supported in part by the Office of Naval Research under contact No. N00014-86-K-0310 and by NIH Grant T15 LM07056 from the National Library of Medicine.