Hardware Accelerated Sequence Alignment with Traceback
Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner. Known methods to accelerate alignment on reconf...
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| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2009-01-01
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| Series: | International Journal of Reconfigurable Computing |
| Online Access: | http://dx.doi.org/10.1155/2009/762362 |
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| _version_ | 1850237153194278912 |
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| author | Scott Lloyd Quinn O. Snell |
| author_facet | Scott Lloyd Quinn O. Snell |
| author_sort | Scott Lloyd |
| collection | DOAJ |
| description | Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results
in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements. |
| format | Article |
| id | doaj-art-01bcdfbc496a49bd93ccb5eceb30b8dd |
| institution | OA Journals |
| issn | 1687-7195 1687-7209 |
| language | English |
| publishDate | 2009-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Reconfigurable Computing |
| spelling | doaj-art-01bcdfbc496a49bd93ccb5eceb30b8dd2025-08-20T02:01:49ZengWileyInternational Journal of Reconfigurable Computing1687-71951687-72092009-01-01200910.1155/2009/762362762362Hardware Accelerated Sequence Alignment with TracebackScott Lloyd0Quinn O. Snell1Department of Computer Science, Brigham Young University, Provo, UT 84602, USADepartment of Computer Science, Brigham Young University, Provo, UT 84602, USABiological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.http://dx.doi.org/10.1155/2009/762362 |
| spellingShingle | Scott Lloyd Quinn O. Snell Hardware Accelerated Sequence Alignment with Traceback International Journal of Reconfigurable Computing |
| title | Hardware Accelerated Sequence Alignment with Traceback |
| title_full | Hardware Accelerated Sequence Alignment with Traceback |
| title_fullStr | Hardware Accelerated Sequence Alignment with Traceback |
| title_full_unstemmed | Hardware Accelerated Sequence Alignment with Traceback |
| title_short | Hardware Accelerated Sequence Alignment with Traceback |
| title_sort | hardware accelerated sequence alignment with traceback |
| url | http://dx.doi.org/10.1155/2009/762362 |
| work_keys_str_mv | AT scottlloyd hardwareacceleratedsequencealignmentwithtraceback AT quinnosnell hardwareacceleratedsequencealignmentwithtraceback |