APPLICATION OF PARALLEL PROCESSING - A CASE STUDY ON DNA SEQUENCE ANALYSIS

Azera Zaid #1, Mohamed Faidz Mohamed Said #2

# Faculty of Computer & Mathematical Sciences, Universiti Teknologi MARA
70300 Seremban, Negeri Sembilan, MALAYSIA

1   azerazaid@gmail.com
2   faidzms@ieee.org

 
Abstract—Most of the analyses of DNA sequences are used by molecular biologists in finding the similarities between dissimilar molecules or in one molecule. Hence, to apply the method of DNA sequence analysis, a program in parallel processing algorithms needs to be written. It allows most present problems to be handled on a medium-sized computer system. This parallel system has been widely recommended to be used for new methods in finding the homology and order in sequences in cases where required information is not readily available.

Keywords: parallel processing, DNA sequence analysis



REFERENCES

[1]	T. Almeida and N. Roma, "A Parallel Programming Framework Formulti-Core DNA Sequence Alignment," n.d.

[2]	T. K. Yap, O. Frieder, S. Member, IEEE, Robert L. Martino, and Member, "Parallel Computation in Biological Sequence Analysis," IEEE Transactions on Parallel and Distributed System, vol. 9, 1998.

[3]	(2017). Columbia Genome Center website [Online ]. Available: https://systemsbiology.columbia.edu/genome-center/sequencing-and-analysis

[4]	J.F.Collins and A.F.W.Coulson, "Applications of Parallel Processing Algorithms for DNA Sequence Analysis," Nucleic Acids Research, vol. 12, pp. 181-192, 1984.

[5]	I. T. M and S. R, "Study of DNA Sequence Analysis Using DSP Techniques," Journal of Automation and Control Engineering, vol. 1, 2013.

[6]	R. Nowak, PiotrWasiewicz, J. J.Mulawka, and A. Plucienniczak, "Processing DNA Tokens in Parallel Computing," 2001.

[7]	P. Frisco. (2011). The Collection of Computer Science Bibliographies website [Online]. Available: http://liinwww.ira.uka.de/bibliography/Misc/dna.html

[8]	E. Hun, M. P. Atkinson, and R. W. Irving, "A Database Index to Large Biological Sequences," Department of Computing Science? University of Glasgow? Glasgow?, n.d.

[9]	K. Ahuja and Kompal, "Analysing Multiple DNA Sequence Alignment Algorithms- Smith Waterman Algorithm and Parallel Smith Waterman Algorithm," International Journal for Research in Applied Science and Engineering Technology (IJraset), vol. 2, 2014.

[10]	(2017). The Wikipedia website [ Online ]. Available: https://en.wikipedia.org/wiki/DNA_sequencing

[11]	PiotrWasiewicz, A. Malinowski, R. Nowak, J. J. Mulawka, P. Borsuk, PiotrWeglenski, et al., "DNA computing: implementation of data flow logical operations," Future Generation Computer Systems, vol. 17, pp. 361-378, 2001.

[12]	(2017). The Wikipedia website [Online]. Available: https://en.wikipedia.org/wiki/GenBank

[13]	(2015). SlideShare website [Online]. Available: https://www.slideshare.net/UsmanAyub6/lecture-no-19

[14]	R. Indumathy and S. U. Maheswari, "Solving DNA Sequence Assembly Using Particle Swarm Optimization with Inertia Weight and Constriction Factor," International Journal of Soft Computing and Artificial Intelligence,, vol. 2, 2014.

[15]	M. F. M. Said, M. N. Taib, and S. Yahya, "Analysis of the CPU Utilization for Point-to-Point Communication Operations in a Beowulf Cluster System," in 2008 International Symposium on Information Technology, 2008, pp. 1-6.

[16]	M. F. M. Said, M. N. Taib, and S. Yahya, "Analysis of TCP/IP Overhead on Overlapping Message Transfer and Computation in a Distributed Memory System Architecture," International Journal of Advanced Research in Computer Science (IJARCS), vol. 3, pp. 22-36, 2012.

[17]	M. F. M. Said, S. Yahya, and M. N. Taib, "Analysis of Different Programming Primitives used in a Beowulf Cluster," International Journal of Computer and Information Technology (IJCIT), vol. 1, pp. 25-33, 2012.