Research Article
Scalable hardware accelerator for comparing DNA and protein sequences
@INPROCEEDINGS{10.1145/1146847.1146880, author={Philippe Faes and Bram Minnaert and Mark Christiaens and Eric Bonnet and Yvan Saeys and Dirk Stroobandt and Yves Van de Peer}, title={Scalable hardware accelerator for comparing DNA and protein sequences}, proceedings={1st International ICST Conference on Scalable Information Systems}, publisher={ACM}, proceedings_a={INFOSCALE}, year={2006}, month={6}, keywords={}, doi={10.1145/1146847.1146880} }- Philippe Faes
Bram Minnaert
Mark Christiaens
Eric Bonnet
Yvan Saeys
Dirk Stroobandt
Yves Van de Peer
Year: 2006
Scalable hardware accelerator for comparing DNA and protein sequences
INFOSCALE
ACM
DOI: 10.1145/1146847.1146880
Abstract
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.