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Among different structural alignment tools, DALIX is one capable of calculating an optimal structural alignment based on the DALI score in most cases. It outperforms DALI, one of the most popular structural alignment algorithms, on the alignment quality. However, the high time complexity of DALIX hinders its application to large protein or complex structure alignments. In this paper, we parallelize...
De Bruijn graph construction is the first step in de novo assemblers to connect input reads into a complete sequence without a reference genome. This step is both time and memory space consuming. To address this problem, we develop ParaHash, a system that partitions the input data in a compact format, parallelizes the computation on both the CPUs and the GPUs in a single computer, and performs hash-based...
We design and implement Mars, a MapReduce framework, on graphics processors (GPUs). MapReduce is a distributed programming framework originally proposed by Google for the ease of development of web search applications on a large number of commodity CPUs. Compared with CPUs, GPUs have an order of magnitude higher computation power and memory bandwidth, but are harder to program since their architectures...
We design and implement Mars, a MapReduce runtime system accelerated with graphics processing units (GPUs). MapReduce is a simple and flexible parallel programming paradigm originally proposed by Google, for the ease of large-scale data processing on thousands of CPUs. Compared with CPUs, GPUs have an order of magnitude higher computation power and memory bandwidth. However, GPUs are designed as special-purpose...
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