Abstract
A parallel Divide-and-Conquer Alignment procedure (DCA) for multiple sequence alignment is presented. DCA improves alignment speed by using the Divide-and-Conquer paradigm, which is suitable for handling large-scale processing problems on multi-core computers. DCA works by dividing the large-scale alignment problem into smaller and more tractable sub-problems which can be solved by the existing algorithms. We assess the execution time and accuracy of our implementation of DCA on an 8-core computer using the classical benchmarks, BAliBASE, PREFAB, IRMBase and OXBENCH, and twenty-eight artificially generated test sets. DCA achieves up to 111-fold improvements in execution time with comparable accuracy.
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