Performance versus Power Analysis for Bioinformatics Sequence Alignment

 

L. Hasan^*, H. Zafar

 

Department of Computer Systems Engineering, University of Engineering and Technology, Peshawar, Pakistan. *laiqhasan@nwfpuet.edu.pk.

 

ABSTRACT

Due to the utilization of abundant hardware resources, power consumption is becoming an important constraint for bioinformatics sequence alignment applications. In this paper, the dynamic power consumption for such applications and its impact on performance is evaluated. Additionally, resource utilization and performance results are provided for implementation with a number of different FPGA platforms. The results obtained using Xilinx ISE tools and Matlab demonstrate that the performance per unit Watt increases rapidly when increasing the number of Processing Elements (PEs). Increasing the number of PEs beyond a certain number slows down the performance per unit Watt significantly. This behavior is used for approximating the number of PEs that gives an optimized performance per unit Watt.

Keywords: Sequence alignment algorithms, FPGAs, performance, dynamic power consumption.

 

DESCARGAR ARTÍCULO EN FORMATO PDF

 

References

[1] M. Vingron and M.S. Waterman, "Sequence Alignment and Penalty Choice: Review of Concepts, Case Studies and Implications", Journal of Molecular Biology, vol. 235, pp. 1-12, 1994.         [ Links ]

[2] A. YarKhan and J.J. Dongarra, "Biological Sequence Alignment on the Computational Grid Using the GrADS Framework", Future Generation Computer Systems, vol. 21, no. 6, pp. 980-986, June 2005.         [ Links ]

[3] L. Hasan, Z. Al-Ars and S. Vassiliadis, "Hardware Acceleration of Sequence Alignment Algorithms - An Overview", Proc. International Conference on Design & Technology of Integrated Systems in Nanoscale Era (DTIS'07), pp. 96-101, Rabat, Morocco, September 2-5, 2007.         [ Links ]

[4] S.F. Altschul, W. Gish, W. Miller, E.W. Myers and D.J. Lipman, "A Basic Local Alignment Search Tool", Journal of Molecular Biology, vol. 215, pp. 403-410, 1990.         [ Links ]

[5] W.R. Pearson and D.J. Lipman, "Rapid and Sensitive Protein Similarity Searches", Science, vol. 227, pp. 1435-1441, 1985.         [ Links ]

[6] S.R. Eddy, "Profile Hidden Morkov Models", Bioinformatics Review, vol. 14, no. 9, pp. 755-763, July 1998.         [ Links ]

[7] R. Giegerich, "A Systematic Approach to Dynamic Programming in Bioinformatics", Bioinformatics, vol. 16, pp. 665-677, 2000.         [ Links ]

[8] T.F. Smith and M.S. Waterman, "Identification of Common Molecular Subsequences", Journal of Molecular Biology, vol. 147, pp. 195-197, 1981.         [ Links ]

[9] L. Hasan and Z. Al-Ars, "An Efficient and High Performance Linear Recursive Variable Expansion Implementation of the Smith-Waterman Algorithm", Proc. 31st Annual International Conference of the IEEE EMBS, pp. 3845-3848, Minneapolis, Minnesota, USA, September 2009.         [ Links ]

[10] A.B. Buyukkur and W. Najjar, "Compiler Generated Systolic Arrays for Wavefront Algorithm Acceleration on FPGAs", Proc. International Conference on Field Programmable Logic and Applications (FPL08), Heidelberg, Germany, September 2008.         [ Links ]

[11] A.D. Blas, D.M. Dahle, M. Diekhans, L. Grate, J. Hirschberg, K. Karplus, H. Keller, M. Kendrick, F.J. Mesa-Martinez, D. Pease, E. Rice, A. Schultz, D. Speck and R. Hughey, "The UCSC Kestrel Parallel Processor", IEEE Transactions on Parallel and Distributed Systems, vol. 16, no. 1, pp. 80-92, 2005.         [ Links ]

[12] W. Liu, B. Schmidt, G. Voss, A. Schroder and W. Muller-Wittig, "Bio-Sequence Database Scanning on a GPU" HICOMB, 2006.         [ Links ]

[13] L. Hasan, Z. Al-Ars, Z. Nawaz and K. L. M. Bertels, "Hardware Implementation of the Smith-Waterman Algorithm Using Recursive Variable Expansion", Proc. 3rd International Design and Test Workshop IDT'08, Monastir, Tunisia, December 2008.         [ Links ]

[14] L. Hasan, Y.M. Khawaja and A. Bais, "A Systolic Array Architecture for The Smith-Waterman Algorithm With High Performance Cell Design", Proc. IADIS European Conference on Data Mining, pp. 35-42, Amsterdam, The Netherlands, July 2008.         [ Links ]

[15] L. Shang, A.S. Kaviani and K. Bathala, "Dynamic Power Consumption in VirtexTM-II FPGA Family", FPGA'02, Monterey, CA, USA, February 24-26, 2002.         [ Links ]

[16] G. Yeap, Practical Low Power Digital VLSI Design, Kluwer Academic Publishers, 1998.         [ Links ]

[17] BioPerf, http://www.bioperf.org/.         [ Links ]

[18] Y. Yu, L.A. Santat and S. Choi, "Bioinformatics packages for sequence analysis", Bioinformatics, vol. 6, pages 143-160, 2006.         [ Links ]

[19] L. Hasan, Z. Al-Ars and M. Taouil, "High Performance and Resource Efficient Biological Sequence Alignment", Proc. 32nd IEEE EMBS, Buenos Aires, Argentina, Aug 31-Sep 4, 2010.         [ Links ]

[20] L. Hasan, M. Kentie and Z. Al-Ars, "DOPA: GPU-based Protein Alignment Using Database and Memory Access Optimizations", Submitted to BMC Bioinformatics, 2011, ISSN 1471-2105.         [ Links ]