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The MicroBlaze processor serves in many FPGA designs as the central 32 bit CPU with access to the global off chip memory and peripherals. MicroBlaze provides FSL links for up to 8 coprocessors. We present two MicroBlaze designs. The first design works with 8 PicoBlaze-based accelerators for pipelined, single-precision floating point vector-oriented operations, and delivers over 1.2 GFLOPs. The second...
Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. The popular BLASTP software for this task has become a bottleneck for proteomic database search. One third of this software's time is spent executing the Smith-Waterman dynamic programming algorithm. This work describes a novel FPGA design for banded Smith-Waterman, an algorithmic variant tuned...
A method is described for enumerating the frequencies of DNA subsequences on a system comprising a host computer and a field programmable gate array (FPGA) board with one FPGA. Frequencies of subsequences with lengths of up to K0 + K1 + K2 (24 in the current implementation) are enumerated in three phases. In these three phases, subsequences with lengths of up to K0, K0 + K1 and K0 + K1 + K2, respectively,...
Knowing the capacitance of circuit nets in an FPGA design is essential when computing the dynamic power consumed by switching these nets. Before a circuit is placed, however, there is little information available to allow the capacitance of routing wires to be estimated. In this paper we study the feasibility of estimating routing capacitance before RTL-synthesis to allow high-level power consumption...
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