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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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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

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