Advantages and GPU implementation of high-performance indexed DNA search based on suffix arrays

@article{Encarnao2011AdvantagesAG,
  title={Advantages and GPU implementation of high-performance indexed DNA search based on suffix arrays},
  author={Gustavo Encarnaç{\~a}o and Nuno Sebasti{\~a}o and Nuno Roma},
  journal={2011 International Conference on High Performance Computing & Simulation},
  year={2011},
  pages={49-55}
}
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… CONTINUE READING
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