Hardware Accelerated Sequence Alignment with Traceback

Scott Lloyd, Quinn O. Snell
2009 International Journal of Reconfigurable Computing  
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
more » ... ed 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.
doi:10.1155/2009/762362 fatcat:hupo7k65sbfafprfxil2e4bjum