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Baagyere, Edward Y.
- A Smith-Waterman Algorithm Accelerator Based on Residue Number System
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1 Kwame Nkrumah University of Science and Technology, Kumasi,, GH
2 University of Development Studies, Navrongo,, GH
1 Kwame Nkrumah University of Science and Technology, Kumasi,, GH
2 University of Development Studies, Navrongo,, GH
Source
International Journal of Electronics and Communication Engineering, Vol 5, No 1 (2012), Pagination: 99-112Abstract
One of the biggest challenges confronting the bioinformatics community is fast and accurate sequence alignment. The Smith-Waterman algorithm (SWA) is one of the several algorithms used in addressing some of these challenges. Though very sensitive in doing sequence alignment, SWA is not used in real life applications due to the computational cost associated with the software implementation. Heuristics methods such as BLAST and FASTA are used, though they do not guarantee accurate sequence alignments. In this paper, we proposed a novel accelerator for addressing the challenge using Residue Number System (RNS). RNS is an integer system with properties that support parallel computation, carry-free addition, borrow-free subtraction, and singlestep multiplication (without partial product). Based on some of these properties, the design of a hardware accelerator for SWA is presented on the assumption that two long strings of DNA can be compared in a divide-andconquer manner. Simulation of a sample design indicates modest hardware consumption and much improved overall speed of the SWA.
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