Abstract

This paper presents an overview and comprehensive survey of Residue Number System (RNS) and Bioinformatics. It focuses on application of RNS to Smith-Waterman Algorithm (SWA), highlights how the inherent attributes of RNS can be applied to improve performance of SWA in the analysis of Deoxyribonucleic Acid (DNA) and also observes the two principal methods of data conversion and lastly, we suggest the direction for future research.

References

• M.A Soderstrand, W.K Jenkins, G. Julliet and F.J Taylor “Residue Number System Arithmetic”, Modern Application in Digital Signal Processing 1986.
• Szabo N.S, Tanaka R.I “ Residue number and its applications to computer technology” McGraw Hill N.Y 1967
• K.A Gbolagade, R. Chares, L. Sousa, S.D Cotofana “ Residue –to- binary converters for the {22n+1-1, 22n, 2n-1} moduli set. 2nd IEEE International conference in adaptive science & technology. Pp 26 – 33 Accra Ghana Dec. 2009
• Neha Singh “ An overview of Residue Number System” National seminar of devices, circuits and communication, Nov 2008
• S. J. Piestrak, "Design of residue generators and multi-operand modular adders using carry-save adders", IEEE Trans. Comput., vol. 423, no. 1, pp. 68-77, Jan. 1994.
• K. M. Elleithy, M. A. Bayoumi, "Fast and flexible architectures for RNS arithmetic decoding", IEEE Trans. Circuits Syst., vol. 39, no. 4, pp. 226-235, Apr. 1992.
• C. H. Huang, "A fully parallel mixed radix conversion algorithm for residue number applications", IEEE Trans. Comput., vol. 32, no. 4, pp. 398-402, Apr. 1983.
• H. M. Yassine, W. R Moore, "Improved mixed-rAdix conversion for residue number system architectures", IEE Proc.-G, vol. 138, no. 1, pp. 120-124, Feb. 1991.
• Bin Cao, Chip-Hong Chang, Thambipillai S. “Adder based residue to binary converters for a new balanced 4-moduli set” Proceedings of the 3rd International Symposium on Image and Signal Processing and analysis (2013)
• Gabriel K A, Emmanuel A, “application of RNS to image processing using orthogonal transformation. Conference Paper · June 2015 DOI: 0.1109/ICCSN.2015.7296177Conference: International Conference on Communications software and Networks
• M. I. Youssef, A. E. Emam, M. Abd Elghany “Multi-Layer Data Encryption using Residue Number System in DNA Sequence” International Journal of Computer Applications (0975 – 8887) Volume 45– No.10, May 2012
• Shahram Moharrami and Davar Kheirandish Taleshmekaeil “The Application of the Residue Number System in Digital Image Processing: Propose a Scheme of Filtering in Spatial Domain “Research Journal of Applied Sciences7: 286-292; DOI: 10.3923/rjasci.2012.286.292;
• Zarandi A.A.E. (2017) RNS Applications in Computer Networks. In: Molahosseini A., de Sousa L., Chang CH. (eds) Embedded Systems Design with Special Arithmetic and Number Systems. Springer, Cham. DOI 10.1007/978-3-319-49742-6_14
• Drashti O. Vadaviya1, Purvi H. Tandel ”Secure Encryption Techniques Using DNA Computation” International Journal of Modern Trends in Engineering and Research (IJMTER) Volume 2, Issue 7, [July-2015] Special Issue of ICRTET’2015.
• Eric B. The importance of DNA in the human cell” pc magazine, New York; 2010. Available:http://sciencing.com/importancedna-human-cell-19447.htm
• Hassan Kehinde Bello and Kazeem Alagbe Gbolagade “A Survey of Human Deoxyribonucleic Acid” British Journal of Applied Science & Technology. 21(5): 1-10, 2017; Article no.BJAST.32463 ISSN: 2231-0843, NLM ID: 101664541; DOI: 10.9734/BJAST/2017/32463
• Jennifer Romeika M, Fei Yan. Recent advances in forensic DNA analysis. J Forensic Res. 2013;S12:001. DOI: 10.4172/2157-7145.S12-001
• Lucia B, Pietro L. Forensic DNA and bioinformatics. Briefings in Bioinformatics. 2007;8(2):117-128. DOI: 10.1093/bib/bbm006 (Advance Access publication March 24, 2007)
• Adrian L, Jennifer EL. Forensic DNA profiling: State of the art. Journal of Research and Reports in Forensic Medical Science. 2014;4:25–36.
• Barbora K, Michael K, Norbert L, Martin F, Marc B, Daniel B, et al. Visualization of biomolecular structures. Eurographics Conference on Visualization (eurovista); 2015. DOI: 0.2312/eurovissta.2015112
• E.Y Baagyere, K.O Boateng, K.A Gbolagade “ Bioinformatics: An important area application of Residue Number System. Journal of Engineering and Applied Sciences 6(2):174-179, 2011
• Miki Y., J. Swensen, D. Shattuck-Eidens, P.A. Futreal and K. Harashman et al 1994. “ A strong candidate for the breast and ovarian cancer susceptibility genes BRCA1. Science 266: 66-71
• Kwame O and Edward Y.B. (2012) “ A smith-waterman algorithm acceleration based on RNS” IJECE ISBN 1974-2166 VOL5 PP99-112
• Laiq Hasan Zaid Al-Ars Zubair Nawaz Koen Bertels “Hardware Implementation of the Smith-Waterman Algorithm Using Recursive Variable Expansion” Delft University of Technology Computer Engineering Laboratory Mekelweg 4, 2628 CD Delft, The Netherlands
• ] Lipman, DJ; Pearson, WR (1985). "Rapid and sensitive protein similarity searches".Science 227 (4693): 1435–41. DOI:10.1126/science.2983426. PMID 2983426
• W. R. Pearson and D. J. Lipman, “Rapid and Sensitive Protein Simlarity Searches”, Science, vol. 227, pp: 1435–1441, 1985.
• S. F. Altschul, Gish, W. Miller, W. Myers and D. J. Lipman, “A Basic Local Alignment Search Tool”, Journal of Molecular Biology, vol. 215, pp: 403–410, 1990
• Altschul Stephen, Gish Warren, Miller Webb, Myers Eugene, Lipman David(1990) “Basic Local Alignment Search tools” Journal of molecular Biology 215(3): 403-410. DOI:10.1016/S0022-2836(05)80360-2 PMID 2231/12
• Smith Temple F., Waterman Michael (1981) “Identification of Common Molecular Subsequences” (PDF).Journal of Molecular biology 147: 195–197. DOI10.1016/0022-2836(81) 90087-5. PMID 7265238
• Gotoh O. “ An improved algorithm for matching biological sequences; Journal of Molecular Biology,162(3):705-708,1982.