A Scalable Hardware Accelerator for Comparing Protein Sequences..
Comparing genetic sequences is a well-known problem
in bio-informatics. Newly discovered 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 FPGA available today.
Faes, P., Minnaert, B., Christiaens, M., Bonnet, E., Saeys, Y., Stroobandt, D., Van de Peer, Y. (2006) A Scalable Hardware Accelerator for Comparing Protein Sequences.. Proceedings of the First International Conference on Scalable Information Systems. Hong Kong, April 2006, on CD.. |
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Contact:
VIB / UGent Bioinformatics & Evolutionary Genomics Technologiepark 927 B-9052 Gent BELGIUM +32 (0) 9 33 13807 (phone) +32 (0) 9 33 13809 (fax) |
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