Massively parallel FPGA-based implementation of BLASTp with the two-hit method

Abstract

Abstract Protein database search requests are generally being performed using the BLASTp algorithm, introduced by NCBI [1] . Since it is computationally intensive, it becomes more and more ine_ective with today's growth of sequence database sizes. The needs for an e_cient parallel implementation arise. In this paper, we focus on a massive parallelization using the FPGA-based hardware architecture RIVYERA [2] . The aim is to reach speedups in orders of magnitude with a flexible implementation while saving energy costs compared to PC-based database search. We keep our implementation close to the structure published by Kasap et al. [3] , [4] and include ideas from Sotiriades et al. [5] such that all parts of the algorithm are organized in components of a long pipeline. We also use the idea of the two-hit method [6] to keep the computational e_ort small. Besides the related work, we perform the very last step of the algorithm to produce a gapped alignment with the Needleman-Wunsch algorithm in software, only with the option of hardware processing after reconfiguration. This saves FPGA-resources and allows an even higher degree of parallelism.