Fatgraph models of RNA structure

Computational and Mathematical Biophysics

Rezazadegan Reza¹  Huang Fenix²  Reidys Christian² 

[1] Biocomplexity Institute of Virginia Tech, 1015 Life Science Circle, VA 24060, Blacksburg, U.S.A., United States of America;Biocomplexity Institute of Virginia Tech, 1015 Life Science Circle, VA 24060, Blacksburg, United States of America;

关键词: rna;    pseudoknot;    fatgraph;    genus;    context free grammar;   

DOI  :  10.1515/mlbmb-2017-0001

来源: DOAJ

【 摘 要 】

In 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.

【 授权许可】

Unknown