WSEAS Transactions on Circuits and Systems
Print ISSN: 1109-2734, E-ISSN: 2224-266X
Volume 14, 2015
A New Processor Array Structure for Protein Sequence Alignment Using Smith-Waterman Algorithm
Authors: , ,
Abstract: This paper proposes a new processor array structure for the Smith-Waterman with affine gap penalty algorithm to align protein sequences. This architecture is extracted by applying a nonlinear mapping methodology to the Smith-Waterman with affine gap penalty algorithm after expressing it as Regular Iterative Algorithm (RIA). This methodology uses a data scheduling and node projection techniques to explore the processor array structures of the algorithm. The proposed structure is one of the explored structures and has the advantage that it can be modified to enable hardware reuse rather than replicating processing elements of the processor array on a cluster of FPGAs. The proposed hardware structure and the previously reported conventional one are described at the Register Transfer Level (RTL) using VHDL language and implemented using the FPGA technology. The implementation results show that the proposed design has significant higher normalized speed-up (up to 124%) over the conventional design for query sequence lengths less than 512 residues. According to the UniProtKB/Swiss-Prot protein knowledgebase (release 2014 07) statistics, the largest number of sequences (about 80%) have sequence length less than 512 residues that makes the proposed design outperforms the conventional design in terms of speed and area in this sequence lengths range.
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Keywords: High performance computing, Parallel processing, Processor arrays, Bio-Computing, Protein sequence alignment, Reconfigurable Computing
Pages: 282-293
WSEAS Transactions on Circuits and Systems, ISSN / E-ISSN: 1109-2734 / 2224-266X, Volume 14, 2015, Art. #33