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A comparative analysis of high-performance implementations of two state of the art index structures that are of particular interest in the field of bioinformatics applications to accelerate the alignment of DNA sequences is presented. The two indexes are based on suffix trees and suffix arrays and were implemented in two different platforms: a quad core CPU and a NVIDIA GeForce GTX 580 GPU, based on the newest Fermi architecture. Unlike what happens in conventional CPU implementations, the obtained experimental results reveal that GPU implementations clearly favor the suffix arrays, due to the achieved performance in terms of memory accesses. When compared with the CPU, the results demonstrate the possibility to achieve speedups as high as 85 when using the suffix array in the GPU, thus making it an adequate choice for high-performance bioinformatics applications.