Table of Contents
ISRN Bioinformatics
Volume 2012, Article ID 195658, 11 pages
Research Article

A Systolic Array-Based FPGA Parallel Architecture for the BLAST Algorithm

1Electrical Engineering and Computer Science Department, The University of Toledo, MS.308, 2801 W. Bancroft Street, Toledo, OH 43607, USA
2Department of Engineering Technology, The University of Toledo, MS.402, 2801 W. Bancroft Street, Toledo, OH 43606, USA

Received 23 May 2012; Accepted 25 July 2012

Academic Editors: F. Couto, B. Haubold, and J. T. L. Wang

Copyright © 2012 Xinyu Guo et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.