The FPGA-based high-performance computer RIVYERA for applications in bioinformatics

Abstract

Bioinformatics specifies a wide field of applications with generally long runtimes or huge amounts of data to be processed - or even both. Typically, large computing clusters or special computing platforms are harnessed to solve problems in this field in reasonable time. One such platform is represented by the FPGA-based high-performance computer RIVYERA, which was intentionally developed for problems in cryptanalysis. On the basis of three easy examples taken from our current research field, we show how RIVYERA can be applied to different kinds of problems regarding bioinformatics. RIVYERA is able to significantly speed up the process of exact sequence alignment using the Smith-Waterman [1] algorithm, querying protein sequence databases using BLASTp [2], and running genome-wide association studies (GWAS) using iLOCI [3] or similar methods based on contingency tables. Likewise, energy savings with RIVYERA are in the same order as runtime reductions compared to standard PCs or computing clusters. © 2014 Springer International Publishing.