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