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In the field of RNA secondary structure prediction, the Zuker algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50% on Zuker. FPGA chips provide a new approach to accelerate the Zuker algorithm by exploiting fine-grained custom design. Zuker...
As one of the most widely used bio-sequence searching tools, 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...
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