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Formal Language Representation and Modelling Structures Underlying RNA Folding Process

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Theoretical Computer Science and Discrete Mathematics (ICTCSDM 2016)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10398))

Abstract

The biological sequences that occur in DNA, RNA and proteins can be considered as strings formed over the well defined chemical alphabets. Such gene sequences form structure based on the complementary pair and the structures can be interpreted as languages. Matrix insertion-deletion system has been introduced a few years back that modelled several bio-molecular structures occur at intramolecular and intermolecular level. In this paper, we identify some structures that are frequently noticed during RNA folding process such as double bulge loop, extended internal loop, triple stem and loop and we give the corresponding formal language representation to such structures. Further, we model the structures using Matrix insertion-deletion systems. This work is pioneering to give the language representation and modelling the structures of RNA folding process using formal grammar.

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References

  1. Brendel, V., Busse, H.G.: Genome structure described by formal languages. Nucleic Acids Res. 12(5), 2561–2568 (1984)

    Article  Google Scholar 

  2. Brown, M., Wilson, C.: RNA Pseudoknot modelling using intersections of stochastic CFG with applications to database search. In: Proceedings of the Pacific Symposium on Biocomputing, Hawaii, USA, pp. 109–125 (1995)

    Google Scholar 

  3. Cai, L., Russell, L., Wu, Y.: Stochastic modelling of RNA pseudoknotted structures: a grammatical approach. Bioinformatics 19(1), 66–73 (2003)

    Article  Google Scholar 

  4. Galiukschov, B.S.: Semicontextual grammars (in Russian). Matem. Logica i Matem. Lingvistika, pp. 38–50 (1981)

    Google Scholar 

  5. Head, T.: Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. Bull. Math. Biol. 49(6), 737–750 (1987)

    Article  MATH  MathSciNet  Google Scholar 

  6. Kari, L., Thierrin, G.: Contextual insertions/deletions and computability. Inf. Comput. 131(1), 47–61 (1996)

    Article  MATH  MathSciNet  Google Scholar 

  7. Kari, L.: On insertion and deletion in formal languages. Ph.D. Thesis, University of Turku (1991)

    Google Scholar 

  8. Kuppusamy, L., Mahendran, A., Krishna, S.N.: Matrix insertion-deletion systems for bio-molecular structures. In: Natarajan, R., Ojo, A. (eds.) ICDCIT 2011. LNCS, vol. 6536, pp. 301–312. Springer, Heidelberg (2011). doi:10.1007/978-3-642-19056-8_23

    Chapter  Google Scholar 

  9. Lakshmanan, K., Anand, M., Clergerie, E.V.: Modelling intermolecular structures and defining ambiguity in gene sequences using matrix insertion-deletion systems. In: Enguix, G.B., Dahl, V., Dolores Jimenez Lopez, M. (eds.) Biology, Computation and Linguistics, New Interdisciplinary Paradigms, pp. 71–85. IOS Press, Amsterdam (2011)

    Google Scholar 

  10. Mamitsuka, H., Abe, N.: Prediction of beta-sheet structures using stochastic tree grammars. In: Proceedings of Fifth Workshop on Genome Informatics, pp. 19–28. Universal Academy Press, Yokohama (1994)

    Google Scholar 

  11. Pan, T., Sosnick, T.: RNA folding during transcription. Annu. Rev. Biophys. Biomol. Struct. 35, 161–175 (2006)

    Article  Google Scholar 

  12. Petre, I., Verlan, S.: Matrix insertion-deletion systems. Theoret. Comput. Sci. 456, 80–88 (2012)

    Article  MATH  MathSciNet  Google Scholar 

  13. Rivas, E., Eddy, S.R.: The language of RNA: a formal grammar that includes pseudoknots. Bioinformatics 16(4), 334–340 (2000)

    Article  Google Scholar 

  14. Rozenberg, G., Salomaa, A.: Handbook of Formal Languages. Springer, New York (1996). doi:10.1007/978-3-642-59126-6

    MATH  Google Scholar 

  15. Searls, D.B.: Representing genetic information with formal grammars. In: Proceedings of the National Conference on Artificial Intelligence, Saint Paul, Minnesota, pp. 386–391 (1988)

    Google Scholar 

  16. 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)

    Google Scholar 

  17. Searls, D.B.: Formal grammars for intermolecular structures. In: First International IEEE Symposium on Intelligence and Biological Systems, Washington, USA, pp. 30–37 (1995)

    Google Scholar 

  18. Searls, D.B.: The language of genes. Nature 420(6912), 211–217 (2002)

    Article  Google Scholar 

  19. Uemura, Y., Hasegawa, A., Kobayashi, S., Yokomori, T.: TAG for RNA structure prediction. Theoret. Comput. Sci. 210(2), 277–303 (1999)

    Article  MATH  MathSciNet  Google Scholar 

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Authors and Affiliations

  1. School of Computer Science and Engineering, VIT University, Vellore, 632014, India

    Anand Mahendran & Lakshmanan Kuppusamy

Authors
  1. Anand Mahendran
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  2. Lakshmanan Kuppusamy
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Corresponding author

Correspondence to Anand Mahendran .

Editor information

Editors and Affiliations

  1. Kalasalingam University, Krishnankoil, India

    S. Arumugam

  2. Ball State University, Muncie, Indiana, USA

    Jay Bagga

  3. Indiana University – Purdue University, Fort Wayne, Indiana, USA

    Lowell W. Beineke

  4. Indian Institute of Technology, New Delhi, India

    B.S. Panda

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Mahendran, A., Kuppusamy, L. (2017). Formal Language Representation and Modelling Structures Underlying RNA Folding Process. In: Arumugam, S., Bagga, J., Beineke, L., Panda, B. (eds) Theoretical Computer Science and Discrete Mathematics. ICTCSDM 2016. Lecture Notes in Computer Science(), vol 10398. Springer, Cham. https://doi.org/10.1007/978-3-319-64419-6_3

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  • DOI: https://doi.org/10.1007/978-3-319-64419-6_3

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-64418-9

  • Online ISBN: 978-3-319-64419-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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