Abstract
Transposable elements (TEs) are DNA sequences that can either move or copy themselves to new positions within a genome. They constitute approximately 45% of the human genome. Knowing the evolution of TEs is helpful in understanding the activities of these elements and their impacts on genomes. In this paper, we devise a formal model providing notations/definitions that are compatible with biological nomenclature, while still providing a suitable formal foundation for computational analysis. We define sequential interruptions between TEs that occur in a genomic sequence to estimate how often TEs interrupt other TEs, useful in predicting their ages. We also define the recursive interruption context-free grammar to capture the recursive nature in which TEs nest themselves into other TEs. We then associate probabilities to convert the context-free grammar into a stochastic context-free grammar, and discuss how to use the CYK algorithm to find a most likely parse tree predicting TE nesting.
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References
Batzer, M., Deininger, P., Hellmann-Blumberg, U., Jurka, J., Labuda, D., Rubin, C., Schmid, C., Zietkiewicz, E., Zuckerkandl, E.: Standardized Nomenclature for Alu Repeats. Journal of Molecular Evolution 42(1), 3–6 (1996)
Belancio, V., Roy-Engel, A., Deininger, P.: All y’all need to know ’bout retroelements in cancer. In: Seminars in Cancer Biology, vol. 20, pp. 200–210. Elsevier (2010)
Durbin, R., Eddy, S., Krogh, A., Mitchison, G.: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge (1998)
Giordano, J., Ge, Y., Gelfand, Y., Abrusán, G., Benson, G., Warburton, P.: Evolutionary History of Mammalian Transposons Determined by Genome-wide Defragmentation. PLoS Computational Biology 3(7), e137 (2007)
Gregory, T.: The Evolution of the Genome. Academic Press (2005)
Hopcroft, J.E.: Introduction to Automata Theory, Languages, and Computation, 3/E. Pearson Education India (2008)
Jones, N.C., Pevzner, P.: An Introduction to Bioinformatics Algorithms. MIT press (2004)
Jurka, J., Kapitonov, V., Pavlicek, A., Klonowski, P., Kohany, O., Walichiewicz, J.: Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research 110(1-4), 462–467 (2005)
Kapitonov, V., Jurkal, J.: The Age of Alu Subfamilies. Journal of Molecular Evolution 42(1), 59–65 (1996)
Kronmiller, B.A., Wise, R.P.: TEnest: Automated Chronological Annotation and Visualization of Nested Plant Transposable Elements. Plant Physiology 146(1), 45–59 (2008)
Lander, E., Linton, L., Birren, B., Nusbaum, C., Zody, M., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al.: Initial Sequencing and Analysis of the Human Genome. Nature 409(6822), 860–921 (2001)
Lerat, E.: Identifying Repeats and Transposable Elements in Sequenced Genomes: How to Find Your Way through the Dense Forest of Programs. Heredity 104(6), 520–533 (2009)
Smit, A., Toth, G., Riggs, A., Jurka, J.: Ancestral, Mammalian-wide Subfamilies of LINE-1 Repetitive Sequences. Journal of Molecular Biology 246(3), 401–417 (1995)
Smit, A.F.A., Hubley, R., Green, P.: RepeatMasker Open-3.0 (1996-2010), http://www.repeatmasker.org
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Jin, L., McQuillan, I. (2013). Computational Modelling of the Interruptional Activities between Transposable Elements. In: Dediu, AH., Martín-Vide, C., Truthe, B., Vega-Rodríguez, M.A. (eds) Theory and Practice of Natural Computing. TPNC 2013. Lecture Notes in Computer Science, vol 8273. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-45008-2_9
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DOI: https://doi.org/10.1007/978-3-642-45008-2_9
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