Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware

  title={Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware},
  author={Timothy F. Oliver and Bertil Schmidt and Yanto Jakop and Douglas L. Maskell},
  booktitle={International Conference on Computational Science},
Profile Hidden Markov Models (PHMMs) are used as a popular tool in bioinformatics for probabilistic sequence database searching. The search operation consists of computing the Viterbi score for each sequence in the database with respect to a given query PHMM. Because of the rapid growth of biological sequence databases, finding fast solutions is of highest importance to research in this area. Unfortunately, the required scan times of currently available sequential software implementations are… CONTINUE READING
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