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International Journal of Reconfigurable Computing
Volume 2009, Article ID 762362, 10 pages
Research Article

Hardware Accelerated Sequence Alignment with Traceback

Department of Computer Science, Brigham Young University, Provo, UT 84602, USA

Received 15 March 2009; Revised 4 August 2009; Accepted 13 October 2009

Academic Editor: Cesar Torres

Copyright © 2009 Scott Lloyd and Quinn O. Snell. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.