Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences Using GPU

  title={Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences Using GPU},
  author={Edans Flavius de Oliveira Sandes and Alba Cristina Magalhaes Alves de Melo},
  journal={IEEE Transactions on Parallel and Distributed Systems},
In Genome Projects, biological sequences are aligned thousands of times, in a daily basis. The Smith-Waterman algorithm is able to retrieve the optimal local alignment with quadratic time and space complexity. So far, aligning huge sequences, such as whole chromosomes, with the Smith-Waterman algorithm has been regarded as unfeasible, due to huge computing and memory requirements. However, high-performance computing platforms such as GPUs are making it possible to obtain the optimal result for… CONTINUE READING
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