Hardware Accelerated Sequence Alignment with Traceback. (3rd December 2009)

• Record Type: Journal Article
• Authors: Lloyd, Scott; Snell, Quinn O.
• Other Names: Torres Cesar Academic Editor.
• Is Part Of: International journal of reconfigurable computing. Volume 2009(2009)
• Publication Date: 2009-12-03
• Subjects: Adaptive computing systems -- Periodicals; Adaptive computing systems; Periodicals; 004
• DOI: 10.1155/2009/762362
• Languages: English
• ISSNs: 1687-7195

Abstract

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.