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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)
Bloom, B.: Space/Time Trade-Offs in Hash Coding with Allowable Errors. Commun. ACM 13(7), 422–426 (1970)
Dharmapurikar, S.: Design and Implementation of a String Matching System for Network Instruction Detection using FPGA-based Bloom Filters. In: Proc. of 12th Annual IEEE symposium on Field Programmable custom Computing Machine (2004)
Kaya, I., Kocak, T.: Energy-Efficient Pipelined Bloom Filters for Network Instruction Detection. In: IEEE international conference on communications 2006, vol. 5, pp. 2382–2387 (2006)
Karishnamurthy, P., Buhler, J., et al.: Biosequence Similarity Search on the Mercury System. Journal of VLSI Signal Processing Systems 49(1), 101–121
Kent, W.J.: BLAT – the BLAST-like alignment tool. Genome Research 12(4), 656–664 (2002)
Ma, B., Tromp, J., Li, M.: PatternHunter: faster and more sensitive homology search. Bioinformatics 18, 440–445 (2002)
Smith, T.F., Waterman, M.S.: Identification of Common Molecular Subsequences. Journal of Molecular Biology 147, 105–197 (1981)
BLAST programs at NCBI, http://www.ncbi.nlm.nih.gov/BLAST/
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Chen, Y., Schmidt, B., Maskell, D.L. (2009). A Reconfigurable Bloom Filter Architecture for BLASTN. In: Berekovic, M., Müller-Schloer, C., Hochberger, C., Wong, S. (eds) Architecture of Computing Systems – ARCS 2009. ARCS 2009. Lecture Notes in Computer Science, vol 5455. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00454-4_7
Download citation
DOI: https://doi.org/10.1007/978-3-642-00454-4_7
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-00453-7
Online ISBN: 978-3-642-00454-4
eBook Packages: Computer ScienceComputer Science (R0)