Fatgraph models of RNA structure

dc.contributor.authorHuang, Fenixen
dc.contributor.authorReidys, Christian Michaelen
dc.contributor.authorRezazadegan, Rezaen
dc.date.accessioned2019-08-23T18:59:45Zen
dc.date.available2019-08-23T18:59:45Zen
dc.date.issued2017-02-08en
dc.description.abstractIn this review paper we discuss fatgraphs as a conceptual framework for RNA structures. We discuss various notions of coarse-grained RNA structures and relate them to fatgraphs. We motivate and discuss the main intuition behind the fatgraph model and showcase its applicability to canonical as well as noncanonical base pairs. Recent discoveries regarding novel recursions of pseudoknotted (pk) configurations as well as their translation into context-free grammars for pk-structures are discussed. This is shown to allow for extending the concept of partition functions of sequences w.r.t. a fixed structure having non-crossing arcs to pk-structures. We discuss minimum free energy folding of pk-structures and combine these above results outlining how to obtain an inverse folding algorithm for PK structures.en
dc.description.notesFormer title of the journal: Molecular Based Mathematical Biologyen
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1515/mlbmb-2017-0001en
dc.identifier.issue1en
dc.identifier.urihttp://hdl.handle.net/10919/93247en
dc.identifier.volume5en
dc.language.isoenen
dc.publisherDe Gruyteren
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivs 3.0 United Statesen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/us/en
dc.subjectRNAen
dc.subjectpseudoknoten
dc.subjectfatgraphen
dc.subjectgenusen
dc.subjectcontext free grammaren
dc.titleFatgraph models of RNA structureen
dc.title.serialComputational and Mathematical Biophysicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen
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