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Original Articles

Performance Evaluation for Field Programmable Gate Array-based Bioinformatics Sequence Alignment

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Pages 17-22 | Published online: 01 Sep 2014

References

  • R Giegerich, “A Systematic Approach to Dynamic Programming in Bioinformatics”, Bioinformatics, Vol. 16, pp. 665–77, 2000.
  • T F Smith, and M S Waterman, “Identification of Common Molecular Subsequences”, Journal of Molecular Biology, Vol. 147, pp. 195–7, 1981.
  • L Hasan, and Z Al-Ars, “An Efficient and High Performance Linear Recursive Variable Expansion Implementation of the Smith-Waterman Algorithm”, 31st Annual International Conference of the IEEE EMBS, Minneapolis, Minnesota, USA, pp. 3845–8, Sept. 2009.
  • A B Buyukkur, and W Najjar, “Compiler Generated Systolic Arrays for Wavefront Algorithm Acceleration on FPGAs”, International Conference on Field Programmable Logic and Applications (FPL08), Heidelberg, Germany, pp. 1–4, Sept. 2008.
  • A. Di Blas, D.M. Dahle, M. Diekhans, L. Grate, J. Hirschberg, and K. Karplus, et al., “The UCSC Kestrel Parallel Processor”, IEEE Transactions on Parallel and Distributed Systems, Vol. 16, pp. 80–92, 2005.
  • W. Liu, B. Schmidt, G. Voss, A. Schroder, and W. Muller-Wittig, “Bio-Sequence Database Scanning on a GPU” HICOMB, pp. 1–8, 2006.
  • L Hasan, Z Al-Ars, Z Nawaz, and K L Bertels, “Hardware Implementation of the Smith-Waterman Algorithm Using Recursive Variable Expansion”, Proceedings of 3rd International Design and Test Workshop IDT’08, Monastir, Tunisia, , pp. 135–40, Dec. 2008.
  • L Hasan, Y M Khawaja, and A Bais, “A Systolic Array Architecture for The Smith-Waterman Algorithm With High Performance Cell Design”, Proceedings of IADIS European Conference on Data Mining, Amsterdam, The Netherlands, pp. 35–42, July 2008.
  • T Oliver, B Schmidt, and D Maskell, “Hyper Customized Processors for Bio-Sequence Database Scanning on FPGAs”, FPGA’05, Monterey, California, USA, pp. 229–37, Feb. 2005.
  • B. Boeckmann, A. Bairoch, R. Apweiler, M. Blatter, A. Estreicher, and E. Gasteiger, et al., “The SWISS-PROT Protein Knowledge Base and its Supplement TrEMBL”, Nucleic Acids Research, Vol. 31, pp. 365–70, 2003.

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