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

Lars Wienbrandt, Stefan Baumgart, Jost Bissel, Florian Schatz, Manfred Schimmler
2011 Procedia Computer Science  
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 ineffective with today's growth of sequence database sizes. The needs for an efficient 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
more » ... ng 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 effort 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.
doi:10.1016/j.procs.2011.04.215 fatcat:qrrxv5qmfnacflc4tru24feh54