Fatgraph models of RNA structure

• Autorzy: Fenix Huang , Christian Reidys , Reza Rezazadegan
• Języki publikacji: EN

Abstrakty

EN

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.

Słowa kluczowe

EN

RNA; pseudoknot; fatgraph; genus; context free grammar

• Wydawca: De Gruyter Open
• Czasopismo: Molecular Based Mathematical Biology
• Rocznik: 2017
• Tom: 5
• Numer: 1
• Strony: 1-20

Daty

wydano

2017-01-01

otrzymano

2016-10-23

zaakceptowano

2016-12-25

online

2017-02-08

Twórcy

autor

Fenix Huang

• Biocomplexity Institute of Virginia Tech, 1015 Life Science Circle, VA 24060, Blacksburg,

autor

Christian Reidys

• Biocomplexity Institute of Virginia Tech, 1015 Life Science Circle, VA 24060, Blacksburg,

autor

Reza Rezazadegan

• Biocomplexity Institute of Virginia Tech, 1015 Life Science Circle, VA 24060, Blacksburg, U.S.A.,

Identyfikatory

DOI

10.1515/mlbmb-2017-0001