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Traditionally, we usually utilize the method of shotgun to cut a DNA sequenceinto pieces and we have to reconstruct the original DNA sequence from thepieces, those are widely used method for DNA assembly. Emerging DNA sequencetechnologies open up more opportunities for molecular biology. This paperintroduce a new method to improve the efficiency of reconstructing DNA sequenceusing suffix array based on CUDA programming model. The experimental resultshow the construction of suffix array using GPU is an more efficient approachon Intel(R) Core(TM) i3-3110K quad-core and NVIDIA GeForce 610M GPU, and studyshow the performance of our method is more than 20 times than that of CPUserial implementation. We believe our method give a cost-efficient solution tothe bioinformatics community.

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA