Abstract
With the greater importance of parallel architectures such as GPUs or Xeon Phi accelerators, the scientific community has developed efficient solutions in the bioinformatics field. In this context, FPGAs begin to stand out as high performance devices with moderate power consumption. This paper presents and evaluates a parallel strategy of the well-known Smith-Waterman algorithm using OpenCL on Intel/Altera’s FPGA for long DNA sequences. We efficiently exploit data and pipeline parallelism on a Intel/Altera Stratix V FPGA reaching upto 114 GCUPS in less than 25 watt power requirements.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Notes
- 1.
Sequences are available in http://www.ncbi.nlm.nih.gov.
- 2.
The symbol ‘-’ indicates an alignment that can not be computed because the optimal score exceeds the corresponding maximum value.
References
Altschul, S.F., Madden, T.L., Schffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acid Res. 25(17), 3389–3402 (1997)
Caffarena, G., Pedreira, C.E., Carreras, C., Bojanic, S., Nieto-Taladriz, O.: FPGA acceleration for DNA sequence alignment. J. Circuits Syst. Comput. 16(2), 245–266 (2007)
Altera Corporation: Altera SDK for OpenCL Programming Guide, v14.0 (2014)
de Oliveira Sandes, E.F., Miranda, G., Alves de Melo, A.C.M., Martorell, X., Ayguadé, E.: CUDAlign 3.0: parallel biological sequence comparison in large GPU clusters. In: CCGRID, pp. 160–169. IEEE Computer Society (2014)
de Oliveira Sandes, E.F., Miranda, G., Martorell, X., Ayguad, E., Teodoro, G., Alves de Melo, A.C.M.: CUDAlign 4.0: incremental speculative traceback for exact chromosome-wide alignment in GPU clusters. IEEE Trans. Parallel Distrib. Syst. 27(10), 2838–2850 (2016)
Feldman, M.: Microsoft goes all in for FPGAs to build out AI cloud (2016). https://www.top500.org/news/microsoft-goes-all-in-for-fpgas-to-build-out-cloud-based-ai/
Gotoh, O.: An improved algorithm for matching biological sequences. J. Mol. Biol. 162, 705–708 (1981)
Khronos Group: The OpenCL Specification, version 2 (2014)
Korpar, M., Sikic, M.: SW# - GPU-enabled exact alignments on genome scale. Bioinformatics 29(19), 2494–2495 (2013)
Leopold, G.: AWS Embraces FPGAs, Elastic GPUs (2016). https://www.hpcwire.com/2016/12/02/aws-embraces-fpgas-elastic-gpus/
Leopold, G.: Intels FPGAs target datacenters, networking (2016). https://www.hpcwire.com/2016/10/06/intels-fpgas-target-datacenters-networking/
Liu, Y., Tran, T.T., Lauenroth, F., Schmidt, B.: SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi coprocessors for long DNA sequences. In: IEEE International Conference on Cluster Computing (CLUSTER), pp. 257–265 (2014)
Mount, D.W.: Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press, Mount (2004)
Pearson, W.R., Lipman, D.J.: Improved tools for biological sequence comparison. Proc. Nat. Acad. Sci. U.S.A. 85(8), 2444–2448 (1988)
Rucci, E., García, C., Botella, G., Giusti, A., Naiouf, M., Prieto-Matías, M.: State-of-the-Art in Smith–Waterman protein database search on HPC platforms. In: Wong, K.-C. (ed.) Big Data Analytics in Genomics, pp. 197–223. Springer, Cham (2016). doi:10.1007/978-3-319-41279-5_6
Rucci, E., Garca, C., Botella, G., De Giusti, A., Naiouf, M., Prieto-Matas, M.: An energy-aware performance analysis of SWIMM: SmithWaterman implementation on Intel’s multicore and manycore architectures. Concurrency Comput. Pract. Exp. 27(18), 5517–5537 (2015)
Rucci, E., Garca, C., Botella, G., De Giusti, A., Naiouf, M., Prieto-Matas, M.: OSWALD: OpenCL Smith-Waterman Algorithm on Altera FPGA for large protein databases. Int. J. High Perform. Comput. Appl. (2016). doi:10.1177/1094342016654215
de Oliveira Sandes, E.F., Alves de Melo, A.C.M: CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences. In: Proceedings of the 15th ACM SIGPLAN Symposium on Principles and Practice of Parallel Computing, PPoPP 2010, pp. 137–146. ACM, New York (2010)
Settle, S.O.: High-performance dynamic programming on FPGAs with OpenCL. In: IEEE High Performance Extreme Computing Conference (HPEC 2013), pp. 1–6 (2013)
Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol. 147(1), 195–197 (1981)
Wienbrandt, L.: Bioinformatics applications on the FPGA-based high-performance computer RIVYERA. In: Vanderbauwhede, W., Benkrid, K. (eds.) High-Performance Computing Using FPGAs, pp. 81–103. Springer, New York (2013). doi:10.1007/978-1-4614-1791-0_3
Yamaguchi, Y., Tsoi, H.K., Luk, W.: FPGA-based Smith-Waterman Algorithm: analysis and novel design. In: Koch, A., Krishnamurthy, R., McAllister, J., Woods, R., El-Ghazawi, T. (eds.) ARC 2011. LNCS, vol. 6578, pp. 181–192. Springer, Heidelberg (2011). doi:10.1007/978-3-642-19475-7_20
Acknowledgments
This work has been partially supported by Spanish government through research contract TIN2015-65277-R and CAPAP-H5 network (TIN2014-53522).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Rucci, E., Garcia, C., Botella, G., De Giusti, A., Naiouf, M., Prieto-Matias, M. (2017). Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA. In: Rojas, I., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2017. Lecture Notes in Computer Science(), vol 10209. Springer, Cham. https://doi.org/10.1007/978-3-319-56154-7_45
Download citation
DOI: https://doi.org/10.1007/978-3-319-56154-7_45
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-56153-0
Online ISBN: 978-3-319-56154-7
eBook Packages: Computer ScienceComputer Science (R0)