Run time reconfiguration of FPGA for scanning genomic databases

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	Similar Articles Articles by E. Lemoine Articles by D. Merceron

IEEE Symposium on FPGA's for Custom Computing Machines (FCCM '95)

Napa Valley, California

April 19-April 21

ISBN: 0-8186-7086-X

	ASCII Text	x
	E. Lemoine, D. Merceron, "Run time reconfiguration of FPGA for scanning genomic databases," Field-Programmable Custom Computing Machines, Annual IEEE Symposium on, pp. 0090, IEEE Symposium on FPGA's for Custom Computing Machines (FCCM '95), 1995.

	BibTex	x
	@article{ 10.1109/FPGA.1995.477414, author = {E. Lemoine and D. Merceron}, title = {Run time reconfiguration of FPGA for scanning genomic databases}, journal ={Field-Programmable Custom Computing Machines, Annual IEEE Symposium on}, volume = {0}, year = {1995}, isbn = {0-8186-7086-X}, pages = {0090}, doi = {http://doi.ieeecomputersociety.org/10.1109/FPGA.1995.477414}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - CONF JO - Field-Programmable Custom Computing Machines, Annual IEEE Symposium on TI - Run time reconfiguration of FPGA for scanning genomic databases SN - 0-8186-7086-X SP EP A1 - E. Lemoine, A1 - D. Merceron, PY - 1995 KW - field programmable gate arrays; database management systems; reduced instruction set computing; performance evaluation; run time reconfiguration; FPGA; genomic databases scanning; performance; genomic sequence databases; XC3090 FPGA; placed Xilinx Netlist File; RISC processor VL - 0 JA - Field-Programmable Custom Computing Machines, Annual IEEE Symposium on ER -

E. Lemoine, Univ. des Sci. et Tech. du Languedoc, Montpellier, France

D. Merceron, Univ. des Sci. et Tech. du Languedoc, Montpellier, France

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/FPGA.1995.477414

Abstract: This paper evaluates the feasibility of reconfiguring an FPGA at run time, and tests its performance using a "Grand Challenge Problem", the high speed scanning of genomic sequence databases. Algorithm implementation into a XC3090 FPGA is described, and methods proposed for generating a placed Xilinx Netlist File that can be efficiently routed at run time by the Automated Placing and Routing Xilinx tools, in order to increase the speed and the density of the design. The same algorithm carefully optimised on a RISC processor has been compared with the run time reconfigurated FPGA, and shows the latter to have an improvement in speed of two to three orders of magnitude.

Index Terms:

field programmable gate arrays; database management systems; reduced instruction set computing; performance evaluation; run time reconfiguration; FPGA; genomic databases scanning; performance; genomic sequence databases; XC3090 FPGA; placed Xilinx Netlist File; RISC processor

Citation:

E. Lemoine, D. Merceron, "Run time reconfiguration of FPGA for scanning genomic databases," fccm, pp.0090, IEEE Symposium on FPGA's for Custom Computing Machines (FCCM '95), 1995

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