A Systolic Array-Based FPGA Parallel Architecture for the BLAST Algorithm. (4th September 2012)

• Record Type: Journal Article
• Authors: Guo, Xinyu; Wang, Hong; Devabhaktuni, Vijay
• Other Names: Couto F. Academic Editor.; Haubold B. Academic Editor.; Wang J. T. L. Academic Editor.
• Is Part Of: ISRN bioinformatics. Volume 2012(2012)
• Publication Date: 2012-09-04
• Subjects: Bioinformatics -- Periodicals; Computational biology -- Periodicals; Medical informatics -- Periodicals; Computational Biology; Medical Informatics; Bioinformatics; Computational biology; Medical informatics; Periodicals; Periodicals; 570.285
• DOI: 10.5402/2012/195658
• Languages: English
• ISSNs: 2090-7338

Abstract

Abstract : A design of systolic array-based Field Programmable Gate Array (FPGA) parallel architecture for Basic Local Alignment Search Tool (BLAST) Algorithm is proposed. BLAST is a heuristic biological sequence alignment algorithm which has been used by bioinformatics experts. In contrast to other designs that detect at most one hit in one-clock-cycle, our design applies a Multiple Hits Detection Module which is a pipelining systolic array to search multiple hits in a single-clock-cycle. Further, we designed a Hits Combination Block which combines overlapping hits from systolic array into one hit. These implementations completed the first and second step of BLAST architecture and achieved significant speedup comparing with previously published architectures.