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Applying Parameterizable Dynamic Configurations to Sequence Alignment
Tom Davidson, Karel Bruneel, Harald Devos, Dirk Stroobandt
616 - 623
10.3233/978-1-60750-530-3-616
Advances in Parallel Computing
Volume 19: Parallel Computing: From Multicores and GPU's to Petascale
Abstract

Hardware acceleration is needed to speed up DNA or protein alignment while keeping the accuracy of the alignment result high enough. The hardware resources used can be effectively optimized by using a new way of run-time reconfiguration, called parameterizable reconfiguration. In this paper, we show how a parameterizable configuration can be used to create a run-time reconfigurable implementation of the Smith-Waterman algorithm. This implementation results in a hardware design that can be implemented on a cheaper FPGA with a performance penalty due to the reconfiguration overhead.

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