Computation of splicing languages from DNA splicing system with one palindromic restriction enzyme
DOI:
https://doi.org/10.11113/mjfas.v14n2.879Keywords:
DNA, palindromic, restriction enzyme, splicing system, C Visual ProgrammingAbstract
In DNA splicing system, the potential effects of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and reassociated to produce further molecules are studied. A splicing language depicts the molecules resulting from a splicing system. In this research, a C++ programming code for DNA splicing system with one palindromic restriction enzyme for one and two (non-overlapping) cutting sites is developed. A graphical user interface, GUI is then designed to allow the user to insert the initial DNA string and restriction enzymes to generate the splicing languages which are the result of the computation of the C++ programming. This interface displays the resulting splicing languages, which depict the results from in vitro experiments of the respective splicing system. The results from this research simplify the lenghty manual computation of the resulting splicing languages of DNA splicing systems with one palindromic restriction enzyme.
References
G. Paun., G. Rozenberg, A. Salomaa, DNA Computing: New Computing Paradigms, Springer -Verlag Berlin Heidelberg, Germany, 1998, p. 1-41.
T. Head, B. Math. Biol, 49 (1987) 737-759.
G. Paun, Discrete. Appl. Math, 70 (1996) 57-79.
D. Pixton, Discrete. App. Math, 69 (1996) 101-124.
E. G. Laun, Constant and Splicing Systems, Ph.D. Thesis, State University of New York at Binghamton, 1999.
Y. Yusof, N. H. Sarmin, W. H. Fong, T. E. Goode, M. A. Ahmad, An Analysis of Four Variants of Splicing System, AIP. Conf. Proc, Putrajaya, Malaysia, 18-20 December 2012, Melville, NY, 2013, p. 888-895.
National Center for Biotechnology Information, Expressed Sequence Tag. Available from: <https://www.ncbi.nlm.nih.gov/nucest>. [11 June 2017].
P. Linz, An Introduction of Formal Language and Automata, John and Barlett Publisher, USA, 2006, p. 1-36.
S. M. Kim, SIAM. J. Comput. 26 (1997) 1284-1309.
I. Tomohiro, S. Inenaga, M. Takeda, Theor. Comput. Sci, 483 (2013) 162-170.
Y. Yusof, DNA Splicing System Inspired by Bio Molecular Operation, Ph.D. Thesis, Universiti Teknologi Malaysia, 2012.
H. M. Eun, Enzymology Primer for Recombinant DNA Technology, Academic Press, USA, 1996, p. 1-108
W. H. Fong, Modelling of Splicing Systems using Formal Language Theory, Ph.D. Thesis, Universiti Teknologi Malaysia, 2008.
T. Head, Discrete. Appl. Math,. 87 (1998) 139-147.
M. H. Mudaber, Y. Yusof, M. S. Mohamad, Some Sufficient Conditions for Persistency and Permanency of Two Stages DNA Splicing Languages via Yusof-Goode Approach, AIP. Conf. Proc, Penang, Malaysia, p. 6-8 November 2013, Melville, NY , 2014, 591-595.
M. A. Ahmad, N. H. Sarmin, Y. Yusof, W. H. Fong, Some Restrictions on the Existence of Second Order Limit Language, AIP. Conf. Proc, Selangor, Malaysia, 24-26 November 2014, Melville, NY, 2015, p. 020048.
W. L. Lim, Y. Yusof, M. H. Mudaber, Modeling of DNA Single Stage Splicing Language via Yusof-Goode Approach: One String with Two Rules, AIP. Conf. Proc, Kuantan, Malaysia, 12-14 August 2014, Melville, NY, 2015, p. 695-699.
New England Biolabs Inc, NEB 2017-18 Catalog & Technical Reference, Catalogue. 2017.
W. H. Fong, N. I. Ismail, Generalisations of DNA Splicing Systems with One Palindromic Restriction Enzyme, Malaysian Journal of Industrial and Applied Mathematics, 2017, Accepted.
