Genome-wide search for coaxial helical stacking motifs

Kevin Byron; Jason T.L. Wang; Dongrong Wen

doi:10.1109/BIBE.2012.6399685

Genome-wide search for coaxial helical stacking motifs

Kevin Byron, Jason T.L. Wang, Dongrong Wen

Computer Science

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

1 Scopus citations

Abstract

Motif finding in DNA, RNA and proteins plays an important role in life science research. In this paper, we present a computational approach to searching for RNA tertiary motifs in genomic sequences. Specifically, we describe a method, named CSminer, and show, as a case study, the application of CSminer to genome-wide search for coaxial helical stackings in RNA 3-way junctions. A coaxial helical stacking motif occurs in an RNA 3-way junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Experimental results demonstrate the effectiveness of our approach.

Original language	English (US)
Title of host publication	IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012
Pages	260-265
Number of pages	6
DOIs	https://doi.org/10.1109/BIBE.2012.6399685
State	Published - 2012
Event	12th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2012 - Larnaca, Cyprus Duration: Nov 11 2012 → Nov 13 2012

Publication series

Name	IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012

Other

Other	12th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2012
Country/Territory	Cyprus
City	Larnaca
Period	11/11/12 → 11/13/12

All Science Journal Classification (ASJC) codes

Bioengineering
Biomedical Engineering

Keywords

RNA junction
coaxial helical stacking
genome-wide motif finding

Access to Document

10.1109/BIBE.2012.6399685

Cite this

@inproceedings{1494ce9079274b79adcb85f1f8c461d0,

title = "Genome-wide search for coaxial helical stacking motifs",

abstract = "Motif finding in DNA, RNA and proteins plays an important role in life science research. In this paper, we present a computational approach to searching for RNA tertiary motifs in genomic sequences. Specifically, we describe a method, named CSminer, and show, as a case study, the application of CSminer to genome-wide search for coaxial helical stackings in RNA 3-way junctions. A coaxial helical stacking motif occurs in an RNA 3-way junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Experimental results demonstrate the effectiveness of our approach.",

keywords = "RNA junction, coaxial helical stacking, genome-wide motif finding",

author = "Kevin Byron and Wang, {Jason T.L.} and Dongrong Wen",

year = "2012",

doi = "10.1109/BIBE.2012.6399685",

language = "English (US)",

isbn = "9781467343589",

series = "IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012",

pages = "260--265",

booktitle = "IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012",

note = "12th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2012 ; Conference date: 11-11-2012 Through 13-11-2012",

}

Byron, K, Wang, JTL & Wen, D 2012, Genome-wide search for coaxial helical stacking motifs. in IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012., 6399685, IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012, pp. 260-265, 12th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2012, Larnaca, Cyprus, 11/11/12. https://doi.org/10.1109/BIBE.2012.6399685

Genome-wide search for coaxial helical stacking motifs. / Byron, Kevin; Wang, Jason T.L.; Wen, Dongrong.
IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012. 2012. p. 260-265 6399685 (IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012).

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

TY - GEN

T1 - Genome-wide search for coaxial helical stacking motifs

AU - Byron, Kevin

AU - Wang, Jason T.L.

AU - Wen, Dongrong

PY - 2012

Y1 - 2012

N2 - Motif finding in DNA, RNA and proteins plays an important role in life science research. In this paper, we present a computational approach to searching for RNA tertiary motifs in genomic sequences. Specifically, we describe a method, named CSminer, and show, as a case study, the application of CSminer to genome-wide search for coaxial helical stackings in RNA 3-way junctions. A coaxial helical stacking motif occurs in an RNA 3-way junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Experimental results demonstrate the effectiveness of our approach.

AB - Motif finding in DNA, RNA and proteins plays an important role in life science research. In this paper, we present a computational approach to searching for RNA tertiary motifs in genomic sequences. Specifically, we describe a method, named CSminer, and show, as a case study, the application of CSminer to genome-wide search for coaxial helical stackings in RNA 3-way junctions. A coaxial helical stacking motif occurs in an RNA 3-way junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Experimental results demonstrate the effectiveness of our approach.

KW - RNA junction

KW - coaxial helical stacking

KW - genome-wide motif finding

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U2 - 10.1109/BIBE.2012.6399685

DO - 10.1109/BIBE.2012.6399685

M3 - Conference contribution

AN - SCOPUS:84872842701

SN - 9781467343589

T3 - IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012

SP - 260

EP - 265

BT - IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012

T2 - 12th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2012

Y2 - 11 November 2012 through 13 November 2012

ER -

Genome-wide search for coaxial helical stacking motifs

Abstract

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Other

All Science Journal Classification (ASJC) codes

Keywords

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