MPI-HMMER-Boost: Distributed FPGA Acceleration

  • John Paul Walters
  • Xiandong Meng
  • Vipin Chaudhary
  • Tim Oliver
  • Leow Yuan Yeow
  • Bertil Schmidt
  • Darran Nathan
  • Joseph Landman


HMMER, based on the profile Hidden Markov Model (HMM) is one of the most widely used sequence database searching tools, allowing researchers to compare HMMs to sequence databases or sequences to HMM databases. Such searches often take many hours and consume a great number of CPU cycles on modern computers. We present a cluster-enabled hardware/software-accelerated implementation of the HMMER search tool hmmsearch. Our results show that combining the parallel efficiency of a cluster with one or more high-speed hardware accelerators (FPGAs) can significantly improve performance for even the most time consuming searches, often reducing search times from several hours to minutes.


HMMER database searching FPGA VLSI MPI profile hidden markov models 


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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • John Paul Walters
    • 1
  • Xiandong Meng
    • 2
  • Vipin Chaudhary
    • 3
  • Tim Oliver
    • 4
  • Leow Yuan Yeow
    • 4
  • Bertil Schmidt
    • 5
  • Darran Nathan
    • 4
  • Joseph Landman
    • 6
  1. 1.Institute for Scientific ComputingWayne State UniversityDetroitUSA
  2. 2.Electrical and Computer Engineering DepartmentWayne State UniversityDetroitUSA
  3. 3.Department of Computer Science and Engineering University at BuffaloThe State University of New YorkBuffaloUSA
  4. 4.Progeniq Pte Ltd.SingaporeSingapore
  5. 5.UNSW AsiaQueenstownSingapore
  6. 6.Scalable Informatics LLCCantonUSA

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