Improved data minimization technique in reducing memory space complexity for DNA local alignment accelerator application

• Published in: 2012 IEEE Symposium on Computer Applications and Industrial Electronics pp. 153 - 156
• Main Authors: Junid, S. A. M. A., Tahir, N. M., Majid, Z. A., Halim, A. K., Shariff, K. K. M.
• Format: Conference Proceeding
• Language: English
• Published: IEEE 01.12.2012
• Subjects: Algorithm design and analysis; Complexity theory; Computer architecture; Data minimization; DNA; DNA sequences alignment; Field programmable gate arrays; FPGA; Hardware design languages; Minimization
• ISBN: 1467330329; 9781467330329
• DOI: 10.1109/ISCAIE.2012.6482087

Improved data minimization technique to optimize the length of DNA sequence and alignment result characters representation is presented in this paper. The primary objective is to improve and optimize data representation for DNA sequences alignment and result character. The proposed design change in algorithm and architecture is presented in this paper. Algorithm design based on binary equivalent method is used to obtain the optimal size of characters representation. The code is written, compiled and simulated using Altera Quartus II Version 9.0 EDA tools. Verilog Hardware Description Language (HDL) and Altera Cyclone II EP2C35 FPGA are used as coding language and target device respectively. In addition, the structural modelling technique is used to reduce the design complexity. Simulation result showed that the improved data minimization technique takes 50% more memory compared to previous work, but it covers 6 DNA sequences and alignment result characters.