Title :
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
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;
Journal_Title :
Design & Test, IEEE
DOI :
10.1109/MDAT.2013.2284191
