Open Access
Issue |
MATEC Web of Conferences
Volume 150, 2018
Malaysia Technical Universities Conference on Engineering and Technology (MUCET 2017)
|
|
---|---|---|
Article Number | 06009 | |
Number of page(s) | 6 | |
Section | Information & Communication Technology (ICT), Science (SCI) & Mathematics (SM) | |
DOI | https://doi.org/10.1051/matecconf/201815006009 | |
Published online | 23 February 2018 |
- F.H.C. Crick, “The Structure of DNA.” Dept. of Biological Syst., The Cavendish Laboratory, Cambridge, England, Tech. Rep. [Google Scholar]
- D.T. Hoang. “FPGA Implementation of Systolic Sequence Alignment,” in International Workshop on Field Programmable Logic and Applications, Vienna, Austria, 1992. [Google Scholar]
- D.T. Hoang, “Searching genetic databases on Splash 2”, in Proceedings of the IEEE Workshop on FPGAs for Custom Computing Machines, 1993, pp. 185–191. [CrossRef] [Google Scholar]
- L. Hasan, Y.M. Khawaja, A. Bais, “A Systolic Array Architecture for The Smith–Waterman Algorithm With High Performance Cell Design”, in Proceedings of IADIS European Conference on Data Mining, Amsterdam, The Netherlands, Jul., 2008. [Google Scholar]
- (2015, Feb. 5). Congressional Justification FY 2015. Retrieved September 24, 2016 from https://www.nlm.nih.gov/about/2015CJ.html. [Google Scholar]
- T.F. Smith and M.S. Waterman. “Identification of Common Molecular Subsequences”, Journal of Molecular Biology, vol. 147, no. 1, pp. 195–197, Mar. 25, 1981. [Google Scholar]
- R. Giegerich, “A Systematic Approach to Dynamic Programming in Bioinformatics.”, Bioinformatics, vol. 16, pp. 665–677, 2000. [CrossRef] [Google Scholar]
- W.R. Pearson, “Using the FASTA Program to Search Protein and DNA Sequence Databases, Computer Analysis of Sequence Data: Part I, Methods in Molecular Biology”, vol. 24, pp. 307–331, 1994. [Google Scholar]
- A. Pulka and A. Milik, “Considerations on Incremental Approach to Hardware Implementation of Smith-Waterman Algorithm,” in Mixed Design of Integrated Circuits and Systems (MIXDES), 2011, IEEE 18th International Conference, pp. 283–288, June 16-18, 2011. [Google Scholar]
- N. Sebastião, N. Roma and P. Flores, “Integrated Hardware Architecture for Efficient Computation of the n-Best Bio-Sequence Local Alignments in Embedded Platforms,” IEEE Transactions on Very Large Scale Integration (VLSI) Systems, vol. 20, no. 7, pp. 1262 – 1275, July,2012. [CrossRef] [Google Scholar]
- H.A. Shah, L. Hasan and N. Ahmad, “An Optimized and Low-cost FPGA-based DNA Sequence Alignment – A Step towards Personal Genomics”, in 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS), pp. 2696 – 2699, July 3 – 7, 2013. [CrossRef] [Google Scholar]
- J. Marmolejo-Tejada, M.V. Trujillo-Olaya, C.P. Rentería-Mejía and J. Velasco-Medina, “Hardware Implementation of the Smith-Waterman Algorithm using a Systolic Architecture”, in Circuits and Systems (LASCAS), 2014 IEEE 5th Latin America Symposium, pp. 1 – 4, February, 2014. [Google Scholar]
- D.S. Nurdin, M.N. Isa, and S.H Goh, “DNA sequence alignment: A review of hardware accelerators and a new core architecture”, in 2016 IEEE 3rd International Conference on Electronic Design (ICED), pp. 264–268, August 11–12, 2016. [CrossRef] [Google Scholar]
- X. Fei, Z. Dan, L. Lina, M. Xin and Z. Chunlei, “FPGASW: Accelerating Large-Scale Smith-Waterman Sequence Alignment Application with Backtracking pn FPGA Linear Systolic Array,” Interdisciplinary Sciences Computational Life Sciences, pp. 1–13, 2017. [Google Scholar]
- T.F. Smith and M.S. Waterman. “Identification of Common Molecular Subsequences,” Journal of Molecular Biology, vol. 147 no. 1, pp. 195–197, Mar. 25, 1981. [Google Scholar]
- O. Gotoh. “An improved algorithm for matching biological sequences”, Journal of Molecular Biology, vol. 162, no. 3, pp. 705, 1982. [CrossRef] [Google Scholar]
- R. Durbin, S. Eddy, A. Krogh and G. Mitchison, Biological Sequence Analysis:Probabilistic Models for Proteins and Nucleic Acids. United Kingdom: Cambridge University Press, 1998. [CrossRef] [Google Scholar]
- K. Benkrid, A. Akoglu, C. Ling, Y. Song, Y. Liu and X. Tian, “High Performance Biological Pairwise Sequence Alignment: FPGA vs. GPU vs. Cell BE vs. GPP,” International Journal of Reconfigurable Computing, Apr., 2012. [Google Scholar]
- C. Fenton, (Aug. 2009,). Final Project Report. [Google Scholar]
- “Advantages of the Virtex-5 FPGA 6-Input LUT Architecture,” Xilinx Inc., 2007. [Google Scholar]
- “FPGA Logic Cell Conversion Ratios,” Galorath Incorporated, 2014. [Google Scholar]
- “Virtex-6 Family Overview”, Xilinx, Inc., 2015. [Google Scholar]
- “FPGA Logic Cells Comparison,” Core technologies. [Google Scholar]
- M. N. Isa, M. I. Ahmad, S. A. Z. Murad, R. C. Ismail, K. Benkrid, “Biological Sequence Alignments: A Review of Hardware Accelerators and a New PE Computing Strategy,” IEEE Region Symposium, pp. 1–6, 2014. [Google Scholar]
Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.
Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.
Initial download of the metrics may take a while.