Combinatorics of RNA-RNA interaction

Thomas J X Li, Christian Reidys

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

308 Downloads (Pure)

Resumé

RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including their generating function, singularity analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number of joint structures.
OriginalsprogEngelsk
TidsskriftJournal of Mathematical Biology
Vol/bind64
Udgave nummer3
Sider (fra-til)529-56
Antal sider28
ISSN0303-6812
DOI
StatusUdgivet - 2012

Fingeraftryk

RNA
Combinatorics
Joints
Interaction
Singularity Analysis
Untranslated RNA
Zigzag
Recurrence relation
Folding
Asymptotic Formula
Generating Function
Diagram
Molecules
Imply
Configuration

Citer dette

Li, Thomas J X ; Reidys, Christian. / Combinatorics of RNA-RNA interaction. I: Journal of Mathematical Biology. 2012 ; Bind 64, Nr. 3. s. 529-56.
@article{526b7cd70ce241f1a4bf255e6290221f,
title = "Combinatorics of RNA-RNA interaction",
abstract = "RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called {"}zigzag{"} configuration. This paper presents the combinatorics of RNA interaction structures including their generating function, singularity analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number of joint structures.",
keywords = "Algorithms, Base Sequence, Combinatorial Chemistry Techniques, Models, Molecular, Molecular Sequence Data, RNA, RNA Folding",
author = "Li, {Thomas J X} and Christian Reidys",
year = "2012",
doi = "10.1007/s00285-011-0423-7",
language = "English",
volume = "64",
pages = "529--56",
journal = "Journal of Mathematical Biology",
issn = "0303-6812",
publisher = "Heinemann",
number = "3",

}

Combinatorics of RNA-RNA interaction. / Li, Thomas J X; Reidys, Christian.

I: Journal of Mathematical Biology, Bind 64, Nr. 3, 2012, s. 529-56.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Combinatorics of RNA-RNA interaction

AU - Li, Thomas J X

AU - Reidys, Christian

PY - 2012

Y1 - 2012

N2 - RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including their generating function, singularity analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number of joint structures.

AB - RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including their generating function, singularity analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number of joint structures.

KW - Algorithms

KW - Base Sequence

KW - Combinatorial Chemistry Techniques

KW - Models, Molecular

KW - Molecular Sequence Data

KW - RNA

KW - RNA Folding

U2 - 10.1007/s00285-011-0423-7

DO - 10.1007/s00285-011-0423-7

M3 - Journal article

C2 - 21541694

VL - 64

SP - 529

EP - 556

JO - Journal of Mathematical Biology

JF - Journal of Mathematical Biology

SN - 0303-6812

IS - 3

ER -