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Book Sections Year : 2011

Modelling Intermolecular Structures and Defining Ambiguity in Gene Sequences using Matrix Insertion-Deletion Systems

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Abstract

Gene insertion and deletion are considered as the basic operations 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. Recently, in [6], a new computing model named Matrix insertion-deletion system has been introduced to model various bio-molecular structures such as hairpin, stem and loop, pseudoknot, attenuator, cloverleaf, dumbbell that occur at intramolecular level. In this paper, we model some of the intermolecular structures such as double strand languages, nick languages, hybrid molecules (with R-loops), holliday structure, replication fork and linear hybridization (ligated) languages using Matrix insertion-deletion system. In [2], the ambiguity in gene sequence was defined as deriving more than one structure for a single gene sequence. Here, we propose a different view of understanding the ambiguity in gene sequences: A gene sequence is obtained by more than one way such that their intermediate sequences are different. We further classify the ambiguity into many levels based on the components axiom, string (order of deletion/insertion) and contexts (order of the used contexts). We notice that some of the inter and intramolecular structures obey the newly defined ambiguity levels.
L'insertion et l'effacement de gènes sont considérés comme les opérations de base dans le traitement de l'ADN et l'édition de l'ARN. Fondé sur ces méchanismes de l'évolution, un modèle de calcul a été formulé dans le cadre de la théorie des langages formels en tant que système d'ajout-effacement. Récemment, un nouveau modèle dénommé "système matriciel d'ajout-effacement" a été introduit pour modéliser différentes structures bio-moléculaires qui apparaissent au niveau intra-moléculaire. Dans ce papier, nous modélisons certaines de ces structures.
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hal-00659487 , version 1 (12-01-2012)

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  • HAL Id : hal-00659487 , version 1

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Lakshmanan Kuppusamy, Anand Mahendran, Éric Villemonte de La Clergerie. Modelling Intermolecular Structures and Defining Ambiguity in Gene Sequences using Matrix Insertion-Deletion Systems. Gemma Bel-Enguix, Veronica Dahl, M. Dolores Jiménez-López. Biology, Computation and Linguistics, new interdisciplinary paradigms, IOS Press, pp.71-82, 2011, Frontiers in Artificial Intelligence and Applications, 978-1-60750-761-1. ⟨hal-00659487⟩
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