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.
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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
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DOI: https://doi.org/10.1007/978-3-642-19056-8_23
Publisher Name: Springer, Berlin, Heidelberg
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