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