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The Viterbi algorithm is the compute-intensive kernel in Hidden Markov Model (HMM) based sequence alignment applications. In this paper, we investigate extending several parallel methods, such as the wave-front and streaming methods for the Smith-Waterman algorithm, to achieve a significant speed-up on a GPU. The wave-front method can take advantage of the computing power of the GPU but it cannot...
Graphics processing units (GPUs) have been widely used to accelerate algorithms that exhibit massive data parallelism or task parallelism. When such parallelism is not inherent in an algorithm, computational scientists resort to simply replicating the algorithm on every multiprocessor of a NVIDIA GPU, for example, to create such parallelism, resulting in embarrassingly parallel ensemble runs that...
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