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	Cyprus
City	Larnaca
Period	11/11/12 → 11/13/12

All Science Journal Classification (ASJC) codes

Bioengineering
Biomedical Engineering

Access to Document

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",

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doi = "10.1109/BIBE.2012.6399685",

language = "English (US)",

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pages = "260--265",

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T1 - Genome-wide search for coaxial helical stacking motifs

AU - Byron, Kevin

AU - Wang, Jason

AU - Wen, Dongrong

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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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DO - 10.1109/BIBE.2012.6399685

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

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