UCT CS Research Document Archive

Accelerating Genomic Sequence Alignment using High Performance Reconfigurable Computers

McMahon, Peter (2008) Accelerating Genomic Sequence Alignment using High Performance Reconfigurable Computers. MSc, Department of Computer Science, University of Cape Town.

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Abstract

Recongurable computing technology has progressed to a stage where it is now possible to achieve orders of magnitude performance and power eciency gains over conventional computer architectures for a subset of high performance computing applications. In this thesis, we investigate the potential of recongurable computers to accelerate genomic sequence alignment specically for genome sequencing applications.

We present a highly optimized implementation of a parallel sequence alignment algorithm for the Berkeley Emulation Engine (BEE2) recongurable computer, allowing a single BEE2 to align simultaneously hundreds of sequences. For each recongurable processor (FPGA), we demonstrate a 61X speedup versus a state-of-the-art implementation on a modern conventional CPU core, and a 56X improvement in performance-per-Watt. We also show that our implementation is highly scalable and we provide performance results from a cluster implementation using 32 FPGAs.

We conclude that recongurable computers provide an excellent platform on which to run sequence alignment, and that clusters of recongurable computers will be able to cope far more easily with the vast quantities of data produced by new ultra-high-throughput sequencers.

EPrint Type:Electronic Thesis or Dissertation
Keywords:Reconfigurable computing, FPGA, bioinformatics, genome sequencing
Subjects:C Computer Systems Organization: C.5 COMPUTER SYSTEM IMPLEMENTATION
C Computer Systems Organization: C.3 SPECIAL-PURPOSE AND APPLICATION-BASED SYSTEMS
J Computer Applications: J.3 LIFE AND MEDICAL SCIENCES
ID Code:505
Deposited By:McMahon, P
Deposited On:27 Febuary 2009