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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.

Citations to this Article [8 citations]

The following is the list of published articles that have cited the current article.

  • M. N. Isa, D. S. Nurdin, M. I. Ahmad, S. A. Z. Murad, S. N. Mohyar, M. Mahyiddin, A. Harun, R. C. Ismail, S. S. Jamuar, and A. Bahari, “DNA sequence alignment: From algorithm to systolic architecture,” 2016 3rd International Conference on Electronic Design (ICED), pp. 304–308, . View at Publisher · View at Google Scholar
  • Le Zheng, Sangho Shin, Scott Lloyd, Maya Gokhale, Kyungmin Kim, and Sung-Mo Kang, “RRAM-based TCAMs for pattern search,” 2016 IEEE International Symposium on Circuits and Systems (ISCAS), pp. 1382–1385, . View at Publisher · View at Google Scholar
  • M. N. Isa, M. I. Ahmad, S. A. Z. Murad, R. C. Ismail, and K. Benkrid, “Biological sequence alignments: A review of hardware accelerators and a new PE computing strategy,” 2014 Ieee Region 10 Symposium, pp. 39–44, . View at Publisher · View at Google Scholar
  • Oleg Medvedev, “Accelerating multiple alignment on FPGA with a high-level hardware description language,” 2011 7th Central and Eastern European Software Engineering Conference (CEE-SECR), pp. 1–7, . View at Publisher · View at Google Scholar
  • Ho-Cheung Ng, Shuanglong Liu, and Wayne Luk, “Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts,” 2017 27th International Conference on Field Programmable Logic and Applications (FPL), pp. 1–8, . View at Publisher · View at Google Scholar
  • Scott Lloyd, and Quinn O. Snell, “Accelerated large-scale multiple sequence alignment,” Bmc Bioinformatics, vol. 12, 2011. View at Publisher · View at Google Scholar
  • Xin Chang, Fernando A. Escobar, Carlos Valderrama, Vincent Robert, Xin Chang, Carlos Valderrama, Fernando A. Escobar, and Vincent Robert, “Optimization strategies for smith-waterman algorithm on FPGA platform,” Proceedings - 2014 International Conference on Computational Science and Computational Intelligence, CSCI 2014, vol. 1, pp. 9–14, 2014. View at Publisher · View at Google Scholar
  • Atef Ibrahim, Hamed Elsimary, and Abdullah Aljumah, “Novel Reconfigurable Hardware Accelerator for Protein Sequence Alignment Using Smith-Waterman Algorithm,” Ieice Transactions On Fundamentals Of Electronics Communications And Computer Sciences, vol. E99A, no. 3, pp. 683–690, 2016. View at Publisher · View at Google Scholar