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

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
Main Authors: Kuppusamy Lakshmanan, Mahendran Anand
Format: Article
Language:English
Published: Sciendo 2016-03-01
Series:International Journal of Applied Mathematics and Computer Science
Subjects:
bio-molecular structures
insertion–deletion systems
intermolecular
intramolecular
secondary structures
Online Access:https://doi.org/10.1515/amcs-2016-0017
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spelling doaj-ada02e3277bd44949f6c4ffc457d42ed2021-09-06T19:39:49ZengSciendoInternational Journal of Applied Mathematics and Computer Science2083-84922016-03-0126124525810.1515/amcs-2016-0017amcs-2016-0017Modelling DNA and RNA secondary structures using matrix insertion–deletion systemsKuppusamy Lakshmanan0Mahendran Anand1School of Computing Science and Engineering, VIT University, Vellore 632014, IndiaDepartment of Computer Science, College of Computer Science and Information Systems, Jazan University, Jazan 45142, Kingdom of Saudi ArabiaInsertion 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.https://doi.org/10.1515/amcs-2016-0017bio-molecular structuresinsertion–deletion systemsintermolecularintramolecularsecondary structures
collection DOAJ
language English
format Article
sources DOAJ
author Kuppusamy Lakshmanan
Mahendran Anand
spellingShingle Kuppusamy Lakshmanan
Mahendran Anand
Modelling DNA and RNA secondary structures using matrix insertion–deletion systems
International Journal of Applied Mathematics and Computer Science
bio-molecular structures
insertion–deletion systems
intermolecular
intramolecular
secondary structures
author_facet Kuppusamy Lakshmanan
Mahendran Anand
author_sort Kuppusamy Lakshmanan
title Modelling DNA and RNA secondary structures using matrix insertion–deletion systems
title_short Modelling DNA and RNA secondary structures using matrix insertion–deletion systems
title_full Modelling DNA and RNA secondary structures using matrix insertion–deletion systems
title_fullStr Modelling DNA and RNA secondary structures using matrix insertion–deletion systems
title_full_unstemmed Modelling DNA and RNA secondary structures using matrix insertion–deletion systems
title_sort modelling dna and rna secondary structures using matrix insertion–deletion systems
publisher Sciendo
series International Journal of Applied Mathematics and Computer Science
issn 2083-8492
publishDate 2016-03-01
description 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.
topic bio-molecular structures
insertion–deletion systems
intermolecular
intramolecular
secondary structures
url https://doi.org/10.1515/amcs-2016-0017
work_keys_str_mv AT kuppusamylakshmanan modellingdnaandrnasecondarystructuresusingmatrixinsertiondeletionsystems
AT mahendrananand modellingdnaandrnasecondarystructuresusingmatrixinsertiondeletionsystems
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