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Suffix array is a simpler and compact alternative to the suffix tree, lexicographic name construction is the fundamental building block in suffix array construction process. This paper depicts the design issues of first data parallel implementation of the lexicographic name construction algorithm on a commodity multiprocessor GPU using the Compute Unified Device Architecture (CUDA) platform, both...
Progressive alignment is a widely used approach for computing multiple sequence alignments (MSAs). However, aligning several hundred or thousand sequences with popular progressive alignment tools such as ClustalW requires hours or even days on state-of-the-art workstations. This paper presents MSA-CUDA, a parallel MSA program, which parallelizes all three stages of the ClustalW processing pipeline...
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