Contraction graphs for representation and analysis of RNA secondary structure

Chris H.Q. Ding; Richard F. Meraz; Xiaofeng He; Stephen R. Holbrook

Contraction graphs for representation and analysis of RNA secondary structure

Chris H.Q. Ding^*, Richard F. Meraz, Xiaofeng He, Stephen R. Holbrook

^*Corresponding author for this work

Lawrence Berkeley National Laboratory

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Scopus citations

Abstract

We introduce the contraction graph as a novel graphical representation of RNA secondary structure. A contraction operation - defined along base pars, single stranded regions, and tertiary interactions - allows for representing RNA secondary structure at different levels of detail. Directionality of the graph and flow conservation of the contraction operation allow for explicit representation of the 5' and 3' ends of the molecule. Furthermore, existing representations such as tree and dual graphs are specific instances in this framework. We anticipate that this unified representation will facilitate automated motif finding and functional classification based on direct searches and comparisons of RNA secondary structure topology.

Original language	English
Title of host publication	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Pages	716-717
Number of pages	2
State	Published - 2004
Externally published	Yes
Event	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 - Stanford, CA, United States Duration: 16 Aug 2004 → 19 Aug 2004

Publication series

Name	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Conference

Conference	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Country/Territory	United States
City	Stanford, CA
Period	16/08/04 → 19/08/04

Cite this

@inproceedings{f5a3e7c1f67048ed9aa99746f271c7c1,

title = "Contraction graphs for representation and analysis of RNA secondary structure",

abstract = "We introduce the contraction graph as a novel graphical representation of RNA secondary structure. A contraction operation - defined along base pars, single stranded regions, and tertiary interactions - allows for representing RNA secondary structure at different levels of detail. Directionality of the graph and flow conservation of the contraction operation allow for explicit representation of the 5' and 3' ends of the molecule. Furthermore, existing representations such as tree and dual graphs are specific instances in this framework. We anticipate that this unified representation will facilitate automated motif finding and functional classification based on direct searches and comparisons of RNA secondary structure topology.",

author = "Ding, \{Chris H.Q.\} and Meraz, \{Richard F.\} and Xiaofeng He and Holbrook, \{Stephen R.\}",

year = "2004",

language = "英语",

isbn = "0769521940",

series = "Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004",

pages = "716--717",

booktitle = "Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004",

note = "Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 ; Conference date: 16-08-2004 Through 19-08-2004",

}

Ding, CHQ, Meraz, RF, He, X & Holbrook, SR 2004, Contraction graphs for representation and analysis of RNA secondary structure. in Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, pp. 716-717, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, Stanford, CA, United States, 16/08/04.

Contraction graphs for representation and analysis of RNA secondary structure. / Ding, Chris H.Q.; Meraz, Richard F.; He, Xiaofeng et al.
Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. 2004. p. 716-717 (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Contraction graphs for representation and analysis of RNA secondary structure

AU - Ding, Chris H.Q.

AU - Meraz, Richard F.

AU - He, Xiaofeng

AU - Holbrook, Stephen R.

PY - 2004

Y1 - 2004

N2 - We introduce the contraction graph as a novel graphical representation of RNA secondary structure. A contraction operation - defined along base pars, single stranded regions, and tertiary interactions - allows for representing RNA secondary structure at different levels of detail. Directionality of the graph and flow conservation of the contraction operation allow for explicit representation of the 5' and 3' ends of the molecule. Furthermore, existing representations such as tree and dual graphs are specific instances in this framework. We anticipate that this unified representation will facilitate automated motif finding and functional classification based on direct searches and comparisons of RNA secondary structure topology.

AB - We introduce the contraction graph as a novel graphical representation of RNA secondary structure. A contraction operation - defined along base pars, single stranded regions, and tertiary interactions - allows for representing RNA secondary structure at different levels of detail. Directionality of the graph and flow conservation of the contraction operation allow for explicit representation of the 5' and 3' ends of the molecule. Furthermore, existing representations such as tree and dual graphs are specific instances in this framework. We anticipate that this unified representation will facilitate automated motif finding and functional classification based on direct searches and comparisons of RNA secondary structure topology.

UR - https://www.scopus.com/pages/publications/14044250175

M3 - 会议稿件

AN - SCOPUS:14044250175

SN - 0769521940

T3 - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

SP - 716

EP - 717

BT - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

T2 - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Y2 - 16 August 2004 through 19 August 2004

ER -

Contraction graphs for representation and analysis of RNA secondary structure

Abstract

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Conference

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