FPGA-based HPRC for bioinformatics applications

Yoshiki Yamaguchi, Yasunori Osana, Masato Yoshimi, Hideharu Amano

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Bioinformatics is one of the most frequently applied fields in FPGAs. Some applications in this field can be efficiently implemented by systolic arrays, which are intrinsically suited to FPGA implementations. Others can be expressed as numerical computations which can parallelize through pipelining, instruction-level and data-level parallelism. This chapter covers two sample applications encountered in bioinformatics, namely homology searches and biochemical molecular simulations, and shows how FPGAs can be effectively harnessed to achieve higher performances compared to off-the-shelf microprocessor technologies.

Original languageEnglish
Title of host publicationHigh-Performance Computing Using FPGAs
PublisherSpringer New York
Pages137-175
Number of pages39
ISBN (Print)9781461417910, 1461417902, 9781461417903
DOIs
Publication statusPublished - 2014 Mar 1

Fingerprint

Bioinformatics
Field programmable gate arrays (FPGA)
Systolic arrays
Microprocessor chips

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Yamaguchi, Y., Osana, Y., Yoshimi, M., & Amano, H. (2014). FPGA-based HPRC for bioinformatics applications. In High-Performance Computing Using FPGAs (pp. 137-175). Springer New York. https://doi.org/10.1007/978-1-4614-1791-0_5

FPGA-based HPRC for bioinformatics applications. / Yamaguchi, Yoshiki; Osana, Yasunori; Yoshimi, Masato; Amano, Hideharu.

High-Performance Computing Using FPGAs. Springer New York, 2014. p. 137-175.

Research output: Chapter in Book/Report/Conference proceedingChapter

Yamaguchi, Y, Osana, Y, Yoshimi, M & Amano, H 2014, FPGA-based HPRC for bioinformatics applications. in High-Performance Computing Using FPGAs. Springer New York, pp. 137-175. https://doi.org/10.1007/978-1-4614-1791-0_5
Yamaguchi Y, Osana Y, Yoshimi M, Amano H. FPGA-based HPRC for bioinformatics applications. In High-Performance Computing Using FPGAs. Springer New York. 2014. p. 137-175 https://doi.org/10.1007/978-1-4614-1791-0_5
Yamaguchi, Yoshiki ; Osana, Yasunori ; Yoshimi, Masato ; Amano, Hideharu. / FPGA-based HPRC for bioinformatics applications. High-Performance Computing Using FPGAs. Springer New York, 2014. pp. 137-175
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