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Sequence Alignment with Traceback on Reconfigurable Hardware

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Permanent URL	http://hdl.lib.byu.edu/1877/2588
Title	Sequence Alignment with Traceback on Reconfigurable Hardware
BYU Creator	Lloyd, Scott Snell, Quinn O.
Keywords	DNA sequencing; traceback; reconfigurable hardware
Description/Abstract	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.
Source	"Sequence Alignment with Traceback on Reconfigurable Hardware", Scott Lloyd and Quinn Snell, In Proceedings of the 2008 International Conference on ReConFigurable Computing and FPGAs (ReConFig'08), Pages 259-264, Dec 2008.;
Publisher	IEEE
Date Original	2008-12
Date Digital	2010-10-14
Language	English eng en
Publication Type	Articles Conference Proceedings
Type	Text
Format	application/pdf
Owning Institution	Brigham Young University
BYU College	College of Physical and Mathematical Sciences
BYU Department	Computer Science
Copyright Status	(c) 2008 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.;
Copyright Use Information	http://www.lib.byu.edu/generic_copyright.html

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