Matrix insertion-deletion systems for bio-molecular structures

  • Authors:

  • Lakshmanan Kuppusamy;Anand Mahendran;Shankara Narayanan Krishna

  • Affiliations:

  • School of Computing Science and Engineering, VIT University, Vellore, India;School of Computing Science and Engineering, VIT University, Vellore, India;Department of Computer Science and Engineering, IIT Bombay, Powai, India

  • Venue:
  • ICDCIT'11 Proceedings of the 7th international conference on Distributed computing and internet technology
  • Year:
  • 2011

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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.