Reconfiguring the Bioinformatics Computational Spectrum: Challenges and Opportunities of FPGA-Based Bioinformatics Acceleration Platforms

Author

Chrysos, Grigorios ; Sotiriades, Euripides ; Rousopoulos, Christos ; Pramataris, Kostas ; Papaefstathiou, Ioannis ; Dollas, Apostolos ; Papadopoulos, Agathoklis ; Kirmitzoglou, Ioannis ; Promponas, Vasilis J. ; Theocharides, Theocharis ; Petihakis, George

Author_Institution

Tech. Univ. of Crete, Chania, Greece

Volume

31

Issue

1

fYear

2014

fDate

Feb. 2014

Firstpage

62

Lastpage

73

Abstract

This paper conducts a detailed survey on the use of FPGA-based reconfigurable computing platforms for a wide range of sequence and structural bioinformatics applications, with emphasis on performance and energy savings of the underlying architectures. Applications considered include sequence comparison, multiple sequence alignment, RNA and protein secondary structure prediction, gene prediction, and phylogenetic tree computation.

Keywords

RNA; bioinformatics; energy conservation; field programmable gate arrays; genetics; molecular biophysics; proteins; FPGA-based bioinformatics acceleration platforms; FPGA-based reconfigurable computing platforms; RNA structure prediction; architecture energy savings; architecture performance; bioinformatics computational spectrum; field programmable gate array; gene prediction; multiple sequence alignment; phylogenetic tree computation; protein secondary structure prediction; sequence bioinformatics applications; sequence comparison; structural bioinformatics applications; Accelerators; Algorithm design and analysis; Bioinformatics; Computational biology; Computer architecture; Field programmable gate arrays; Hardware; Software algorithms;

fLanguage

English

Journal_Title

Design & Test, IEEE

Publisher

ieee

ISSN

2168-2356

Type

jour

DOI

10.1109/MDAT.2013.2284191

Filename

6617681