<abstract xmlns="http://www.w3.org/1999/xhtml"><p>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 <italic>matrix insertion–deletion system,</italic> and using it we model several bio-molecular structures that occur at the intramolecular, intermolecular and RNA secondary levels.</p></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.

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

School of Computing Science and Engineering, VIT University, Vellore 632014, India

Department of Computer Science, College of Computer Science and Information Systems, Jazan University, Jazan 45142, Kingdom of Saudi Arabia

International Journal of Applied Mathematics and Computer Science

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Insertion and deletion are operations that occur commonly in DNA processing and RNA editing. Since biological macromolecules can be viewed as symbols, gene...

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

Published Online: Mar 31, 2016

Page range: 245 - 258

Received: Aug 08, 2014

DOI: https://doi.org/10.1515/amcs-2016-0017

Keywords
bio-molecular structures, insertion–deletion systems, intermolecular, intramolecular, secondary structures

© 2016 Lakshmanan Kuppusamy et al., published by De Gruyter Open

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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

Published Online: Mar 31, 2016

Page range: 245 - 258

Received: Aug 08, 2014

DOI: https://doi.org/10.1515/amcs-2016-0017

Keywordsbio-molecular structures, insertion–deletion systems, intermolecular, intramolecular, secondary structures

© 2016 Lakshmanan Kuppusamy et al., published by De Gruyter Open

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Keywords
bio-molecular structures, insertion–deletion systems, intermolecular, intramolecular, secondary structures