Fatgraph models of RNA structure

Fenix Huang, Christian Reidys, and Reza Rezazadegan. "Fatgraph models of RNA structure." Molecular Based Mathematical Biology 5.1 (2017): 1-20. <http://eudml.org/doc/288047>.

@article{FenixHuang2017,
abstract = {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.},
author = {Fenix Huang, Christian Reidys, Reza Rezazadegan},
journal = {Molecular Based Mathematical Biology},
keywords = {RNA; pseudoknot; fatgraph; genus; context free grammar},
language = {eng},
number = {1},
pages = {1-20},
title = {Fatgraph models of RNA structure},
url = {http://eudml.org/doc/288047},
volume = {5},
year = {2017},
}

TY - JOUR
AU - Fenix Huang
AU - Christian Reidys
AU - Reza Rezazadegan
TI - Fatgraph models of RNA structure
JO - Molecular Based Mathematical Biology
PY - 2017
VL - 5
IS - 1
SP - 1
EP - 20
AB - 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.
LA - eng
KW - RNA; pseudoknot; fatgraph; genus; context free grammar
UR - http://eudml.org/doc/288047
ER -