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Accelerating genomic sequence alignment using high performance reconfigurable computers
Includes bibliographical references (pages 65-70).
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| Main Author: | |
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| Other Authors: | |
| Format: | Thesis |
| Language: | English |
| Published: |
Department of Computer Science
2016
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| _version_ | 1867613330738249728 |
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| access_status_str | Open Access |
| author | McMahon, Peter Leonard |
| author2 | Kuttel, Michelle Mary |
| author_browse | Kuttel, Michelle Mary McMahon, Peter Leonard |
| author_facet | Kuttel, Michelle Mary McMahon, Peter Leonard |
| author_sort | McMahon, Peter Leonard |
| collection | Thesis |
| description | Includes bibliographical references (pages 65-70). |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/17377 |
| institution | University of Cape Town (South Africa) |
| language | eng |
| last_indexed | 2026-06-10T12:34:25.395Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| publisher | Department of Computer Science |
| publisherStr | Department of Computer Science |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/17377 Accelerating genomic sequence alignment using high performance reconfigurable computers McMahon, Peter Leonard Kuttel, Michelle Mary Computer Science Includes bibliographical references (pages 65-70). Reconfigurable 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. 2016-02-29T12:07:18Z 2016-02-29T12:07:18Z 2008 Master Thesis Masters MSc http://hdl.handle.net/11427/17377 eng application/pdf Department of Computer Science Faculty of Science University of Cape Town |
| spellingShingle | Computer Science McMahon, Peter Leonard Accelerating genomic sequence alignment using high performance reconfigurable computers |
| thesis_degree_str | Master's |
| title | Accelerating genomic sequence alignment using high performance reconfigurable computers |
| title_full | Accelerating genomic sequence alignment using high performance reconfigurable computers |
| title_fullStr | Accelerating genomic sequence alignment using high performance reconfigurable computers |
| title_full_unstemmed | Accelerating genomic sequence alignment using high performance reconfigurable computers |
| title_short | Accelerating genomic sequence alignment using high performance reconfigurable computers |
| title_sort | accelerating genomic sequence alignment using high performance reconfigurable computers |
| topic | Computer Science |
| url | http://hdl.handle.net/11427/17377 |
| work_keys_str_mv | AT mcmahonpeterleonard acceleratinggenomicsequencealignmentusinghighperformancereconfigurablecomputers |