The Java Programming Language
Efficient memory management for hardware accelerated Java Virtual Machines
ACM Transactions on Design Automation of Electronic Systems (TODAES)
Hardware accelerated sequence alignment with traceback
International Journal of Reconfigurable Computing - Special issue on selected papers from ReConFig 2008
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Comparing genetic sequences is a well-known problem in bioinformatics. Newly determined sequences are being compared to known sequences stored in databases in order to investigate biological functions. In recent years the number of available sequences has increased exponentially. Because of this explosion a speedup in the comparison process is highly required. To meet this demand we implemented a dynamic programming algorithm for sequence alignment on reconfigurable hardware. The algorithm we implemented, Smith-Waterman-Gotoh (SWG) has not been implemented in hardware before. We show a speedup factor of 40 in a design that scales well with the size of the available hardware. We also demonstrate the limits of larger hardware for small problems, and project our design on the largest Field Programmable Gate Array (FPGA) available today.