Scalable and highly parallel implementation of Smith-Waterman on graphics processing unit using CUDA

@article{Akoglu2009ScalableAH,
  title={Scalable and highly parallel implementation of Smith-Waterman on graphics processing unit using CUDA},
  author={Ali Akoglu and Gregory M. Striemer},
  journal={Cluster Computing},
  year={2009},
  volume={12},
  pages={341-352}
}
Program development environments have enabled graphics processing units (GPUs) to become an attractive high performance computing platform for the scientific community. A commonly posed problem in computational biology is protein database searching for functional similarities. The most accurate algorithm for sequence alignments is Smith-Waterman (SW). However, due to its computational complexity and rapidly increasing database sizes, the process becomes more and more time consuming making… CONTINUE READING
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