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International Journal of Reconfigurable Computing
Volume 2009, Article ID 762362, 10 pages
Research Article

Hardware Accelerated Sequence Alignment with Traceback

Department of Computer Science, Brigham Young University, Provo, UT 84602, USA

Received 15 March 2009; Revised 4 August 2009; Accepted 13 October 2009

Academic Editor: Cesar Torres

Copyright © 2009 Scott Lloyd and Quinn O. Snell. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. C. Macken, H. Lu, J. Goodman, and L. Boykin, “The value of a database in surveillance and vaccine selection,” in Options for the Control of Influenza IV, vol. 1219 of International Congress Series, pp. 103–106, October 2001. View at Google Scholar
  2. S. N. Gardner, M. W. Lam, N. J. Mulakken, C. L. Torres, J. R. Smith, and T. R. Slezak, “Sequencing needs for viral diagnostics,” Journal of Clinical Microbiology, vol. 42, no. 12, pp. 5472–5476, 2004. View at Google Scholar
  3. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994. View at Google Scholar
  4. C. Notredame, D. G. Higgins, and J. Heringa, “T-coffee: a novel method for fast and accurate multiple sequence alignment,” Journal of Molecular Biology, vol. 302, no. 1, pp. 205–217, 2000. View at Google Scholar
  5. S. B. Needleman and C. D. Wunsch, “A general method applicable to the search for similarities in the amino acid sequence of two proteins,” Journal of Molecular Biology, vol. 48, no. 3, pp. 443–453, 1970. View at Google Scholar
  6. T. F. Smith and M. S. Waterman, “Identification of common molecular subsequences,” Journal of Molecular Biology, vol. 147, no. 1, pp. 195–197, 1981. View at Google Scholar
  7. T. Ramdas and G. Egan, “A survey of FPGAs for acceleration of high performance computing and their application to computational molecular biology,” in Proceedings of the IEEE Region 10 Annual International Conference (TENCON '05), pp. 1–6, Melbourne, Australia, November 2005. View at Publisher · View at Google Scholar
  8. P. Chain, S. Kurtz, E. Ohlebusch, and T. Slezak, “An applications-focused review of comparative genomics tools: capabilities, limitations and future challenges,” Briefings in Bioinformatics, vol. 4, no. 2, pp. 105–123, 2003. View at Google Scholar
  9. F. Delsuc, H. Brinkmann, and H. Philippe, “Phylogenomics and the reconstruction of the tree of life,” Nature Reviews Genetics, vol. 6, no. 5, pp. 361–375, 2005. View at Publisher · View at Google Scholar · View at PubMed
  10. T. Slezak, T. Kuczmarski, L. Ott et al., “Comparative genomics tools applied to bioterrorism defence,” Briefings in Bioinformatics, vol. 4, no. 2, pp. 133–149, 2003. View at Google Scholar
  11. O. Gotoh, “An improved algorithm for matching biological sequences,” Journal of Molecular Biology, vol. 162, no. 3, pp. 705–708, 1982. View at Google Scholar
  12. E. W. Myers and W. Miller, “Optimal alignments in linear space,” Computer Applications in the Biosciences, vol. 4, no. 1, pp. 11–17, 1988. View at Google Scholar
  13. D. T. Hoang and D. P. Lopresti, “FPGA implementation of systolic sequence alignment,” in Field-Programmable Gate Arrays: Architectures and Tools for Rapid Prototyping, H. Grünbacher and R. W. Hartenstein, Eds., pp. 183–191, Springer, Berlin, Germany, 1992. View at Google Scholar
  14. R. P. Jacobi, M. Ayala-Rincón, L. G. Carvalho, C. H. Llanos, and R. W. Hartenstein, “Reconfigurable systems for sequence alignment and for general dynamic programming,” Genetics and Molecular Research, vol. 4, no. 3, pp. 543–552, 2005. View at Google Scholar
  15. T. VanCourt and M. C. Herbordt, “Families of FPGA-based accelerators for approximate string matching,” Microprocessors and Microsystems, vol. 31, no. 2, pp. 135–145, 2007. View at Publisher · View at Google Scholar
  16. Y. Yamaguchi, T. Maruyama, and A. Konagaya, “High speed homology search with FPGAs,” in Proceedings of the 7th Pacific Symposium on Biocomputing (PSB '02), pp. 271–282, Lihue, Hawaii, USA, January 2002.
  17. G. L. Moritz, C. Jory, H. S. Lopes, and C. R. E. Lima, “Implementation of a parallel algorithm for protein pairwise alignment using reconfigurable computing,” in Proceedings of the IEEE International Conference on Reconfigurable Computing and FPGA's (ReConFig '06), pp. 99–105, San Luis Potosi, Mexico, September 2006. View at Publisher · View at Google Scholar
  18. K. Benkrid, Y. Liu, and A. Benkrid, “A highly parameterized and efficient FPGA-based skeleton for pairwise biological sequence alignment,” IEEE Transactions on Very Large Scale Integration (VLSI) Systems, vol. 17, no. 4, pp. 561–570, 2009. View at Publisher · View at Google Scholar
  19. E. W. Edmiston, N. G. Core, J. H. Saltz, and R. M. Smith, “Parallel processing of biological sequence comparison algorithms,” International Journal of Parallel Programming, vol. 17, no. 3, pp. 259–275, 1988. View at Publisher · View at Google Scholar
  20. X. Guan and E. C. Uberbacher, “A multiple divide-and-conquer (MDC) algorithm for optimal alignments in linear space,” Tech. Rep. ORNL/TM-12764, Oak Ridge National Lab., June 1994. View at Google Scholar
  21. R. Lipton and D. Lopresti, “Comparing long strings on a short systolic array,” in Systolic Arrays, W. Moore, A. McCabe, and R. Urquhart, Eds., pp. 363–376, Hilger, Bristol, UK, 1987. View at Google Scholar
  22. S. Lloyd and Q. Snell, “Qnet: a modular architecture for reconfigurable computing,” in Proceedings of the International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA '08), pp. 259–265, Las Vegas, Nev, USA, July 2008.
  23. C. Sanderson, “Simplify FPGA application design with DIMEtalk,” Xcell Journal, vol. 51, pp. 104–107, 2004. View at Google Scholar
  24. PCI-SIG, “PCI Express,”
  25. P. Faes, B. Minnaert, M. Christiaens et al., “Scalable hardware accelerator for comparing DNA and protein sequences,” in Proceedings of the 1st International Conference on Scalable Information Systems (INFOSCALE '06), ACM, Hong Kong, May-June 2006.
  26. Seq-Gen,
  27. S. Rajko and S. Aluru, “Space and time optimal parallel sequence alignments,” IEEE Transactions on Parallel and Distributed Systems, vol. 15, no. 12, pp. 1070–1081, 2004. View at Publisher · View at Google Scholar