Towards a Shape Language for Interpreting RNA Folding

Adane Mamuye; Emanuela Merelli; Luca Tesei

9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)

Research Article

Towards a Shape Language for Interpreting RNA Folding

Cite: BibTeX Plain Text

@INPROCEEDINGS{10.4108/eai.3-12-2015.2262523,
    author={Adane Mamuye and Emanuela Merelli and Luca Tesei},
    title={Towards a Shape Language for Interpreting RNA Folding},
    proceedings={9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)},
    publisher={ACM},
    proceedings_a={BICT},
    year={2016},
    month={5},
    keywords={rna secondary structures rna shapes s[b] paradigm formal languages group theory topological data analysis},
    doi={10.4108/eai.3-12-2015.2262523}
}

Adane Mamuye
Emanuela Merelli
Luca Tesei
Year: 2016
Towards a Shape Language for Interpreting RNA Folding
BICT
EAI
DOI: 10.4108/eai.3-12-2015.2262523

Adane Mamuye¹, Emanuela Merelli¹, Luca Tesei¹^,*

1: School of Science and Technology, University of Camerino

*Contact email: luca.tesei@unicam.it

Abstract

In this paper we introduce a shape language for representing RNA secondary structures in a non-standard, non-linear way. The main motivation is to propose a new interpretation of RNA folding as a self-adaptability process, within the S[B] paradigm, towards a minimum free energy configuration. An RNA secondary structure is decomposed first by distinguishing between pseudoknot free and pseudonotted sub-structures. For pseudoknot free sub-structures a proper formal language is defined. To address the representation of pseudoknotted sub-structures the crucial aspects of RNA irreducible shapes and their associated automatic groups are introduced.

Keywords: rna secondary structures rna shapes s[b] paradigm formal languages group theory topological data analysis

Published: 2016-05-24
Publisher: ACM

: http://dx.doi.org/10.4108/eai.3-12-2015.2262523