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Paper details
Number 1 - March 2016
Volume 26 - 2016
Modelling DNA and RNA secondary structures using matrix insertion–deletion systems
Lakshmanan Kuppusamy, Anand Mahendran
Abstract
Insertion and deletion are operations that occur commonly in DNA processing and RNA editing. Since biological macromolecules can be viewed as symbols, gene sequences can be represented as strings and structures can be interpreted as
languages. This suggests that the bio-molecular structures that occur at different levels can be theoretically studied by formal
languages. In the literature, there is no unique grammar formalism that captures various bio-molecular structures. To
overcome this deficiency, in this paper, we introduce a simple grammar model called the matrix insertion–deletion system, and using it we model several bio-molecular structures that occur at the intramolecular, intermolecular and RNA secondary levels.
Keywords
bio-molecular structures, insertion–deletion systems, intermolecular, intramolecular, secondary structures