Opportunities from the use of FPGAs as platforms for bioinformatics algorithms

TitleOpportunities from the use of FPGAs as platforms for bioinformatics algorithms
Publication TypeConference Publication
Year of Publication2012
AuthorsChrysos, G, Sotiriades E, Rousopoulos C, Dollas A, Papadopoulos A, Kirmitzoglou I, Promponas V, Theocharides T, Petihakis G, Lagnel J, Vavylis P, Kotoulas G
Conference NameIEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012
Pages559 - 565
Date Published2012///
KeywordsBioinformatics algorithms, FPGA based systems, high performance

This paper presents an in-depth look of how FPGA computing can offer substantial speedups in the execution of bioinformatics algorithms, with specific results achieved to date for a broad range of algorithms. Examples and case studies are presented for sequence comparison (BLAST, CAST), multiple sequence alignment (MAFFT, T-Coffee), RNA and protein secondary structure prediction (Zuker, Predator), gene prediction (Glimmer/GlimmerHMM) and phylogenetic tree computation (RAxML), running on mainstream FPGA technologies as well as high-end FPGA-based systems (Convey HC1, BeeCube). This work also presents technological and other obstacles that need to be overcome in order for FPGA computing to become a mainstream technology in Bioinformatics. © 2012 IEEE.


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