Show simple item record

Accelerating genomic sequence alignment using high performance reconfigurable computers

dc.contributor.advisorKuttel, Michelle Maryen_ZA
dc.contributor.authorMcMahon, Peter Leonarden_ZA
dc.descriptionIncludes bibliographical references (pages 65-70).en_ZA
dc.description.abstractReconfigurable computing technology has progressed to a stage where it is now possible to achieve orders of magnitude performance and power efficiency gains over conventional computer architectures for a subset of high performance computing applications. In this thesis, we investigate the potential of reconfigurable computers to accelerate genomic sequence alignment specifically for genome sequencing applications. We present a highly optimized implementation of a parallel sequence alignment algorithm for the Berkeley Emulation Engine (BEE2) reconfigurable computer, allowing a single BEE2 to align simultaneously hundreds of sequences. For each reconfigurable 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 reconfigurable computers provide an excellent platform on which to run sequence alignment, and that clusters of reconfigurable computers will be able to cope far more easily with the vast quantities of data produced by new ultra-high-throughput sequencers.en_ZA
dc.subject.otherComputer Scienceen_ZA
dc.titleAccelerating genomic sequence alignment using high performance reconfigurable computersen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.publisher.facultyFaculty of Scienceen_ZA
dc.publisher.departmentDepartment of Computer Scienceen_ZA

Files in this item


This item appears in the following Collection(s)

Show simple item record