Coupling hundreds of workstations for parallel molecular sequence analysis

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Abstract
We present a highly scalable approach to distributed parallel computing on workstations in the Internet which provides significant speed‐up to molecular biology sequence analysis. Recent developments show that smaller numbers of workstations connected via a local area network can be used efficiently for parallel computing. This work emphasizes scalability with respect to the number of workstations employed. We show that a massively parallel approach using several hundred workstations, dispersed over all continents, can successfully be applied for solving problems with low requirements on communication bandwidth. We calculated the optimal local alignment scores between a single genetic sequence and all sequences of a genetic sequence database using the ssearch code that is well known among molecular biologists. In a heterogeneous network with more than 800 workstations this job terminated after several minutes, in contrast to several days it would have taken on a single machine.

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