NDLI: Design of a FPGA-Based Parallel Architecture for BLAST Algorithm with Multi-hits Detection

Content Provider	IEEE Xplore Digital Library
Author	Xinyu Guo Hong Wang Devabhaktuni, V.
Copyright Year	2011
Abstract	In this paper, a design of a Field Programmable Gate Array (FPGA)-based parallel architecture for Basic Local Alignment Search Tool (BLAST) Algorithm with multi-hits Detection is proposed. Basic Local Alignment Search Tool algorithm is a heuristic biological sequence alignment algorithm and has been widely used in the computational biology domain. The architecture contains several different blocks. Each block will perform a different step of National Center for Biotechnology Information (NCBI) BLAST family algorithms in parallel. The most appealing and distinguishing features of this architecture are the Multiple Hits Finder Array and Hits Combination Block. In the hits detection stage, we apply a Multiple Hits Finder Array approach to realize the multi-hits in one clock cycle. Then the multiple overlapping hits are merged together in the Hits Finder Block to reduce memory consumption and save implementation time. The parallel design makes this FPGA-based BLAST algorithm implementation much faster than an equivalent software program would in a PC. Multiple Hits Finder Array architecture prototype is implemented and the storage expense and synthesis performance of the prototype are discussed.
Starting Page	689
Ending Page	694
File Size	241780
Page Count	6
File Format	PDF
ISBN	9781612844275
DOI	10.1109/ITNG.2011.122
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-04-11
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Algorithm design and analysis FPGA-based Architecture Overlapping Hits Combination Software algorithms BLAST Algorithm Multiple Hits Detection Logic gates Biology Parallel Arrays Field programmable gate arrays
Content Type	Text
Resource Type	Article

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