A Pattern Matching Approach for the Estimation of Alignment Between Any Two Given DNA Sequences
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For a given DNA sequence, it is well known that pair wise alignment schemes are used to determine the similarity with the DNA sequences available in the databanks. The efficiency of the alignment decides the type of amino acids and its corresponding proteins. In order to evaluate the given DNA sequence for its proteomic identity, a pattern matching approach is proposed in this paper. A block based semi-global alignment scheme is introduced to determine the similarity between the DNA sequences (known and given). The two DNA sequences are divided into blocks of equal length and alignment is performed which minimizes the computational complexity. The efficiency of the alignment scheme is evaluated using the parameter, percentage of similarity (POS). Four essential DNA version of the amino acids that emphasize the importance of proteomic functionalities are chosen as patterns and matching is performed with the known and given DNA sequences to determine the similarity between them. The ratio of amino acid counts between the two sequences is estimated and the results are compared with that of the POS value. It is found from the experimental results that higher the POS value and the pattern matching higher are the similarity between the two DNA sequences. The optimal block is also identified based on the POS value and amino acids count.
KeywordsAmino acids DNA Sequence alignment Semi-global alignment Pattern matching
- 3.Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J., Basic local alignment search tool. J. Mol. Biol. 215:403–410, 1990.Google Scholar
- 5.Setubal, J., and Meidanis, J., Introduction to computational molecular biology. PWS Company: Boston, MA, 1997.Google Scholar
- 9.Basu, K., Sriraam, N., and Richard, R. J. A., Global alignment of two DNA sequences: Mechanism and strategy. In: Proceeding of International Medical Informatics and Biomedical Engineering Symposium (IMIBE’06), March 20–23, 2006, Jordan.Google Scholar
- 10.Basu, K., Sriraam, N., and Richard, R. J. A., Block based semi-global alignment scheme for the analysis of given DNA sequences. In: World Congress on Medical Physics and Biomedical Engineering, South Korea, September 2006.Google Scholar
- 11.DNA Data Bank of Japan DDBJ: http://www.ddbj.nig.ac.jp/.
- 12.Maloy, S. R., Cronan (Jr.), J. E., and Freifelder, D., Microbial genetics. Jones and Bartlett: Boston, MA, pp. 29–55, 1994.Google Scholar
- 13.Wilson, K., and Walker, J., Principles and techniques of biochemistry and molecular biology, 6th edition. Cambridge University Press: Cambridge, UK, pp. 166–179, 2005.Google Scholar