Hardware Accelerated Sequence Alignment with Traceback | Zendy

Scott Lloyd | Zendy; Quinn Snell | Zendy

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Hardware Accelerated Sequence Alignment with Traceback

Author(s) -

Scott Lloyd,

Quinn Snell

Publication year - 2009

Publication title -

international journal of reconfigurable computing

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.236

H-Index - 16

eISSN - 1687-7209

pISSN - 1687-7195

DOI - 10.1155/2009/762362

Subject(s) - computer science , sequence (biology) , scalability , field programmable gate array , parallel computing , computer hardware , limit (mathematics) , architecture , algorithm , biology , operating system , art , mathematical analysis , genetics , mathematics , visual arts

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 resultsin 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

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