Abstract:BLAST adopts index-based approach to detect the matches between two substrings by looking up a large table and processing one match per query. In this paper, we propose a systolic array approach to detect string matches without using looking up tables. The pipelining systolic array is implemented as a multi-seeds detection and parallel extension engine to accelerate the first two stages of NCBI BLAST algorithm. Different from the index-based approach, our implementation consumes little memory resources and eli… Show more
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