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

Guo X, Wang H, Devabhaktuni V - ISRN Bioinform (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Electrical Engineering and Computer Science Department, The University of Toledo, MS.308, 2801 W. Bancroft Street, Toledo, OH 43607, USA.

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.

No MeSH data available.


Exponential growth of biological sequence database on a yearly basis.
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Related In: Results  -  Collection


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fig1: Exponential growth of biological sequence database on a yearly basis.

Mentions: Being one of the most important tools applied in finding biological sequence alignment, BLAST (Basic Local Alignment Search Tool) [4] has been widely implemented on commodity PC clusters. But with the exponential growth of the biosequence databases (see Figure 1 [1]), meeting the computational requirements using current platforms is becoming a difficult task.


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

Guo X, Wang H, Devabhaktuni V - ISRN Bioinform (2012)

Exponential growth of biological sequence database on a yearly basis.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4417556&req=5

fig1: Exponential growth of biological sequence database on a yearly basis.
Mentions: Being one of the most important tools applied in finding biological sequence alignment, BLAST (Basic Local Alignment Search Tool) [4] has been widely implemented on commodity PC clusters. But with the exponential growth of the biosequence databases (see Figure 1 [1]), meeting the computational requirements using current platforms is becoming a difficult task.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Electrical Engineering and Computer Science Department, The University of Toledo, MS.308, 2801 W. Bancroft Street, Toledo, OH 43607, USA.

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.

No MeSH data available.