Hardware oriented optimization of Smith-Waterman algorithm
Adam Milik, Andrzej Pułka · ICSES 2010 International Conference on Signals and Electronic Circuits · 2010
The work presented within the paper concerns very important problem of searching for string alignments. The problem originates from modern computation biology. Hardware based implementations have been driving out software solutions in the field recently. The complex programmable devices have become very commonly applied. The paper introduces a new, optimized approach based on Smith-Waterman dynamic programming algorithm. The original algorithm is modified in order to simplify the datapath processing and take advantage of the properties offered by FPGA devices. The results obtained with the proposed methodology allow reducing the size of the functional block and radically speed up the processing time. This approach is very competitive compared with other related works.