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Protein sequences with unknown functionality are often compared to a set of known sequences to detect functional similarities. Efficient dynamic programming algorithms exist for this problem, however current solutions still require significant scan times. These scan time requirements are likely to become even more severe due to the rapid growth in the size of these databases. In this paper, we present a new approach to bio-sequence database scanning using computer graphics hardware to gain highdoi:10.1109/ipdps.2006.1639531 dblp:conf/ipps/LiuSVSM06 fatcat:ltjk4qzmm5aenm4vadamvlb5be