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This paper presents HMMer-Cell, an implementation of the computationally intensive bioinformatics application HMMER on the Cell/B.E. multiprocessor architecture. The core of the HMMER workload is the Plan7 Viterbi algorithm, which has a memory requirement of O(N*M) where N is the length of the HMM and M is the length of the input sequence length. The main challenge in implementing the Plan7 Viterbi...
Microprocessors are becoming increasingly susceptible to soft errors due to the current trends of semiconductor technology scaling. Traditional redundant multi-threading architectures provide good fault tolerance by re-executing all the computations. However, such a full re-execution significantly increases the demand on the processor resources, resulting in severe performance degradation. To address...
Recent advances in bioinformatics and the significant increase in computational power available to researchers have made it possible to make better use of the vast amounts of genetic data that has been collected over the last two decades. As the uses of genetic data expand to include drug discovery and development of gene-based therapies, bioinformatics is destined to take its place in the forefront...
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