%0 Journal Article
%T Hardware Accelerated Sequence Alignment with Traceback
%A Scott Lloyd
%A Quinn O. Snell
%J International Journal of Reconfigurable Computing
%D 2009
%I Hindawi Publishing Corporation
%R 10.1155/2009/762362
%X 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.
%U http://www.hindawi.com/journals/ijrc/2009/762362/