Abstract
Insertion and deletion are considered to be the basic operations in Biology, more specifically in DNA processing and RNA editing. Based on these evolutionary transformations, a computing model has been formulated in formal language theory known as insertion-deletion systems. Since the biological macromolecules can be viewed as symbols, the gene sequences can be represented as strings. This suggests that the molecular representations can be theoretically analyzed if a biologically inspired computing model recognizes various bio-molecular structures like pseudoknot, hairpin, stem and loop, cloverleaf and dumbbell. In this paper, we introduce a simple grammar system that encompasses many bio-molecular structures including the above mentioned structures. This new grammar system is based on insertion-deletion and matrix grammar systems and is called Matrix insertion-deletion grammars. Finally, we discuss how the ambiguity levels defined for insertion-deletion grammar systems can be realized in bio-molecular structures, thus the ambiguity issues in gene sequences can be studied in terms of grammar systems.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Salomaa, A.: Formal languages. Academic Press, New York (1973)
Brendel, V., Busse, H.G.: Genome structure described by formal languages. Nucleic Acids Res., 2561–2568 (1984)
Calude, C.S., Paŭn, G.: Computing with cells and atoms, An intro. to Quantum, DNA and Membrane Computing. Taylor and Francis, London (2001)
Searls, D.B.: Representing genetic information with formal grammars. In: Proceedings of the National Conference on Artificial Intelligence, pp. 386–391 (1988)
Searls, D.B.: The linguistics of DNA. American Scientist, 579–591 (1992)
Searls, D.B.: The computational linguistics of biological sequences. In: Hunter, L. (ed.) Artificial Intelligence and Molecular Biology, pp. 47–120. AAAI Press, Menlo Park (1993)
Rivas, E., Reddy, S.R.: The language of RNa: A formal grammar that includes psuedoknots. Bioinformatics 16, 334–340 (2000)
Păun, G., Rozenberg, G., Salomaa, A.: DNA Computing, New Computing Paradigms. Springer, Heidelberg (1998)
Păun, G.: Membrane Computing-An introduction. Springer, Heidelberg (2002)
Hopcroft, J.E., Motwani, R., Ullman, J.D.: Introduction to Automata Theory, Languages and Computation. Addison-Wesley, Reading (2006)
Krithivasan, K., Kuppusamy, L., Mahendran, A.: On the ambiguity and complexity measures in insertion-deletion systems. In: Proceedings of Bionetics-2010, USA, December 1-3. LNCS (2010)
Rozenberg, G., Salomaa, A.: Handbook of formal languages. Springer, Heidelberg (1997)
Verlan, S.: On minimal context-free insertion-deletion systems. Journal of Automata, Languages and Combinatorics 2, 317–328 (2007)
Setubal., J.C., Meidanis, J.: Introduction to Computational Molecular Biology. PWS Publishing Company (1997)
Uemura, Y., Hasegawa, A., Kobayashi, S., Yokomori, T.: Tree adjoining grammarsfor RNA structure prediction. Theoretical Computer Science 210, 277–303 (1999)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kuppusamy, L., Mahendran, A., Krishna, S.N. (2011). Matrix Insertion-Deletion Systems for Bio-Molecular Structures. In: Natarajan, R., Ojo, A. (eds) Distributed Computing and Internet Technology. ICDCIT 2011. Lecture Notes in Computer Science, vol 6536. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19056-8_23
Download citation
DOI: https://doi.org/10.1007/978-3-642-19056-8_23
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-19055-1
Online ISBN: 978-3-642-19056-8
eBook Packages: Computer ScienceComputer Science (R0)