Genome-wide search for coaxial helical stacking motifs

Kevin Byron; Jason Wang; Dongrong Wen

doi:10.1109/BIBE.2012.6399685

Genome-wide search for coaxial helical stacking motifs

Kevin Byron, Jason Wang, Dongrong Wen

Computer Science

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

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 - Dec 1 2012
Event	12th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2012 - Larnaca, Cyprus Duration: Nov 11 2012 → Nov 13 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

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10.1109/BIBE.2012.6399685

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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.",

author = "Kevin Byron and Jason Wang and Dongrong Wen",

year = "2012",

month = dec,

day = "1",

doi = "10.1109/BIBE.2012.6399685",

language = "English (US)",

isbn = "9781467343589",

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",

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TY - GEN

T1 - Genome-wide search for coaxial helical stacking motifs

AU - Byron, Kevin

AU - Wang, Jason

AU - Wen, Dongrong

PY - 2012/12/1

Y1 - 2012/12/1

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.

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U2 - 10.1109/BIBE.2012.6399685

DO - 10.1109/BIBE.2012.6399685

M3 - Conference contribution

AN - SCOPUS:84872842701

SN - 9781467343589

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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