DNA sequence matching processor using FPGA and JAVA interface

Author

Brown, Benjamin O. ; Yin, Meng-Lai ; Cheng, Yi

Author_Institution

Dept. of Electr. Eng., California State Polytech. Univ., Pomona, CA, USA

Volume

2

fYear

2004

fDate

1-5 Sept. 2004

Firstpage

3043

Lastpage

3046

Abstract

This study uses an FPGA to perform high-speed DNA sequence matching as an alternative to using general purpose computer CPUs. The FPGA is programmed using the Verilog HDL and interfaced using a graphical user interface programmed in JAVA. Design overviews and details for a small scale design are given as well as plans for larger scale expansion. Encouraging results of the small scale model currently in production are also provided. Results of a successful match and no match are shown.

Keywords

DNA; Java; biology computing; digital computers; field programmable gate arrays; genetics; graphical user interfaces; hardware description languages; molecular biophysics; parallel processing; DNA sequence matching processor; FPGA; JAVA; JAVA interface; Verilog HDL; computer CPU; graphical user interface; parallel processing; Computer interfaces; DNA; Databases; Field programmable gate arrays; Graphical user interfaces; Hardware design languages; Java; Parallel processing; Registers; Sequences; Exact matching; FPGA; HDL; JAVA; parallel processing;

fLanguage

English

Publisher

ieee

Conference_Titel

Engineering in Medicine and Biology Society, 2004. IEMBS '04. 26th Annual International Conference of the IEEE

Conference_Location

San Francisco, CA

Print_ISBN

0-7803-8439-3

Type

conf

DOI

10.1109/IEMBS.2004.1403861

Filename

1403861