AN EFFICIENT CORE ARCHITECTURE FOR PROTEIN SEQUENCE ALIGNMENT

This paper presents efficient biological sequence alignment core architecture to reduce execution time of the well-known dynamic programming-based (DP) pairwise sequence alignment algorithms i.e. the Smith Waterman algorithm. The PE was prototyped in the Xilinx Virtex 5 FPGA with further improvement...

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Bibliographic Details
Published in:ARPN journal of engineering and applied sciences 2015-10, Vol.10 (18), p.8311-8314
Main Authors: Nazrin, Mohd, Isa, Md, Murad, Sohiful Anuar Zainol, Ismail, Rizalafande Che, Jambek, Asral Bahari
Format: Article
Language:English
Subjects:
Algorithms
Alignment
Architecture
Field programmable gate arrays
Hardness
Hardware
Proteins
Strategy
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Summary:This paper presents efficient biological sequence alignment core architecture to reduce execution time of the well-known dynamic programming-based (DP) pairwise sequence alignment algorithms i.e. the Smith Waterman algorithm. The PE was prototyped in the Xilinx Virtex 5 FPGA with further improvements have been done in the scheduling strategy of alignment matrix computation and substitution coefficients' pre-loading onto the processing elements in folded systolic arrays. Implementation rresults showed that the new hardware architecture for the protein sequence alignment achieved over 100x speed-up performance, compared to the well-known SSEARCH 35 'software-only implementation' and more than ~1.6x speed up improvement against our previously implemented core in Virtex 5 FPGA.
ISSN:1819-6608
1819-6608