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IPPS
2006
IEEE

Parallel implementation and performance characterization of MUSCLE

13 years 9 months ago
Parallel implementation and performance characterization of MUSCLE
Multiple sequence alignment is a fundamental and very computationally intensive task in molecular biology. MUSCLE, a new algorithm for creating multiple alignments of protein sequences, achieves a highest rank in accuracy and the fastest speed compared to ClustalW as well as T-Coffee, some widely used tools in multiple sequence alignment. To further accelerate the computations, we present the parallel implementation of MUSCLE in this paper. It is decomposed into several independent modules, which are parallelized with different OpenMP paradigms. We also conduct detailed performance characterization on symmetric multiple processor systems. The experiments show that MUSCLE scales well with the increase of processors, and achieves up to 15.x speedup on 16-way shared memory multiple processor system.
Xi Deng, Eric Li, Jiulong Shan, Wenguang Chen
Added 12 Jun 2010
Updated 12 Jun 2010
Type Conference
Year 2006
Where IPPS
Authors Xi Deng, Eric Li, Jiulong Shan, Wenguang Chen
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