MODELLING OF TWO STAGES DNA SPLICING LANGUAGES ON DE BRUIJN GRAPH
DOI:
https://doi.org/10.11113/jt.v78.4236Keywords:
de Bruijn graph, permanent, persistent, two stages splicing languages, Y-G splicing systemAbstract
Finding the sequence of the genome from its compositions as well as a mathematical graph is the most interesting topic in a field of DNA molecular. Since lack of technology is the big obstacle that biologists are facing to read a long sequence of the genome from beginning up to the end, therefore finding the compositions of the genome having very long sequence and also its description via de Bruijn graph is challenging or even impossible. In this paper, Yusof-Goode (Y-G) approach is used to generate the DNA splicing languages based on cutting sites of initial strings (one or two cutting sites) and crossing and contexts factors of restriction enzymes. The two short sequences of DNA (8bp) and two restriction enzymes are considered to create a connection between mathematics and DNA molecular.  This relation will be presented as de Bruijn graph so that every edge of the de Bruijn graph gives a k-mer composition of DNA molecule and also each path of the de Bruijn graph gives a DNA sequence and vice-versa. Besides, the persistency and permanency of two stages DNA splicing languages can be predicted using this model.
References
Robin, S., Rondolphe, F and Schbath, S. 2006. DNA World and Model. UK. Cambridge University Press.
Walker, J. M. and Rapley, R. 2009. Molecular Biology and Biotechnology. London: Royal Society of Chemistry.
Kaptcianos, J. 2008. A Graph Theoretical Aapproach to DNA Fragment Assembly. American Journal of Undergraduate Research. 7(1): ISSN 1536-4558.
Pevzner, P. A. and Tang, H. 2001. Fragment Assembly with Double-Barreled Data. Bioinformatics. 17: 225-233.
Medvedev, P. and Brudno, M. 2009. Maximum Likehood Genome Assembly. Journal of Computational Biology. 16: 1101-1116.
Jinn, L. S., Fong, W. H., Sarmin, N. H. and Karimi, Fariba. 2011. Mathematical Modelling of Some Null-Context and Uniform Splicing System. Journal of Fundamental and Applied Sciences. 7(2): 145-149.
Fong, W.H., Sarmin, N.H. and Ibrahim, Z. 2009. Recognition of Simple Splicing System Using SH-Automata. Journal of Fundamental and Applied Sciences. 4(2): 337-342.
Mudaber, M.H., Yusof, Y. and Mohamad, S. M. Some Relations between Two Stages DNA Splicing Languages. AIP Conf. Proc. 1602: 254-259.
Yusof, Y. 2012. DNA Splicing System Inspired by Bio Molecular Operation. Ph.D. Thesis. Universiti Teknilogi Malaysia.
Linz, P. 2006. An Introduction to Formal Languages Theory and Automata. USA. Jones and Barlett Publisher.
Head, T. 1987. Formal Language Theory and DNA: An Analysis of the Generative Capacity of Specific Recombinant Behaviors. Bulletin of Mathematical Biology. 49(6): 737-759.
Gatterdam, R. 1992. Algorithm for Splicing System. SIAM Journal of Computing. 21(3): 507-520.
Pevzner, P., Conpeau, P. E. C. and Vyahhi, Nikolay. 2013. How to Assemble Genome? Bioinformatics Algorithms. (online) https://www.coursera.org/-course/bioinformatics.
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