A Reconfigurable Bloom Filter Architecture for BLASTN

Authors:
Yupeng Chen;Bertil Schmidt;Douglas L. Maskell
Affiliations:
School of Computer Engineering, Nanyang Technological University, Singapore;School of Computer Engineering, Nanyang Technological University, Singapore;School of Computer Engineering, Nanyang Technological University, Singapore
Venue:
ARCS '09 Proceedings of the 22nd International Conference on Architecture of Computing Systems
Year:
2009

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Abstract

Efficient seed-based filtration methods exist for scanning genomic sequence databases. However, current solutions require a significant scan time on traditional computer architectures. These scan time requirements are likely to become even more severe due to the rapid growth in the size of databases. In this paper, we present a new approach to genomic sequence database scanning using reconfigurable field-programmable gate array (FPGA)-based hardware. To derive an efficient mapping onto this type of architecture, we propose a reconfigurable Bloom filter architecture. Our experimental results show that the FPGA implementation achieves an order of magnitude speedup compared to the NCBI BLASTN software running on a general purpose computer.