High Speed Homology Search Using Run-Time Reconfiguration

@inproceedings{Yamaguchi2002HighSH,
  title={High Speed Homology Search Using Run-Time Reconfiguration},
  author={Yoshiki Yamaguchi and Yosuke Miyajima and Tsutomu Maruyama and Akihiko Konagaya},
  booktitle={FPL},
  year={2002}
}
In this paper, we show a new approach for homology search based on run-time reconfiguration. In our approach, the search consists of two phases, and different circuits are configured on demand during the search to make up for the limited memory bandwidth of off-theshelf FPGA boards. Experiments with an off-the-shelf FPGA (Xilinx XCV2000E) board showed good results. The time for comparing a query sequence of 2,048elemen ts with a database sequence of 64 million elements by the Smith-Waterman… CONTINUE READING

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