{"title":"Towards a Shape Language for Interpreting RNA Folding","authors":"A. Mamuye, E. Merelli, L. Tesei","doi":"10.4108/EAI.3-12-2015.2262523","DOIUrl":null,"url":null,"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. \n \nAn 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.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"19 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"International Conference on Bio-inspired Information and Communications Technologies","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.4108/EAI.3-12-2015.2262523","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 1
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.