An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases

@article{Ligowski2009AnEI,
  title={An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases},
  author={Lukasz Ligowski and Witold R. Rudnicki},
  journal={2009 IEEE International Symposium on Parallel & Distributed Processing},
  year={2009},
  pages={1-8}
}
The Smith Waterman algorithm for sequence alignment is one of the main tools of bioinformatics. It is used for sequence similarity searches and alignment of similar sequences. The high end Graphical Processing Unit (GPU), used for processing graphics on desktop computers, deliver computational capabilities exceeding those of CPUs by an order of magnitude. Recently these capabilities became accessible for general purpose computations thanks to CUDA programming environment on Nvidia GPUs and ATI… CONTINUE READING

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