Modelling DNA and RNA secondary structures using matrix insertion–deletion systems

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 occ...

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Bibliographic Details
Published in:International journal of applied mathematics and computer science 2016-03, Vol.26 (1), p.245-258
Main Authors: Kuppusamy, Lakshmanan, Mahendran, Anand
Format: Article
Language:English
Subjects:
bio-molecular structures
insertion–deletion systems
intermolecular
intramolecular
secondary structures
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Summary: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 and using it we model several bio-molecular structures that occur at the intramolecular, intermolecular and RNA secondary levels.
ISSN:2083-8492
1641-876X
2083-8492
DOI:10.1515/amcs-2016-0017