Constrained RNA structural alignment: Algorithms and application to motif detection in the untranslated regions of Trypanosoma brucei mRNAs

Mugdha Khaladkar; Vivian Bellofatto; Jason T.L. Wang; Vandanaben Patel; Marvin K. Nakayama

doi:10.1109/BIBE.2007.4375585

Constrained RNA structural alignment: Algorithms and application to motif detection in the untranslated regions of Trypanosoma brucei mRNAs

Mugdha Khaladkar, Vivian Bellofatto, Jason T.L. Wang, Vandanaben Patel, Marvin K. Nakayama

Computer Science

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

Abstract

In this paper we propose a new method for aligning two RNA secondary structures by taking into account the presence of conserved RNA substructures, or constraints, in the alignment process. Our method allows the incorporation of specific knowledge about the RNA structures being analyzed while computing their alignment and thus is very useful for RNA motif detection. We develop statistical measures to assess the significance of alignment scores. Experimental results obtained by using the constrained alignment method to search for structural motifs in the untranslated regions of Trypanosoma brucei mRNAs demonstrate the good performance of the proposed method and its superiority over existing methods.

Original language	English (US)
Title of host publication	Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Pages	334-341
Number of pages	8
DOIs	https://doi.org/10.1109/BIBE.2007.4375585
State	Published - 2007
Event	7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE - Boston, MA, United States Duration: Jan 14 2007 → Jan 17 2007

Publication series

Name	Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Other

Other	7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Country/Territory	United States
City	Boston, MA
Period	1/14/07 → 1/17/07

All Science Journal Classification (ASJC) codes

Biotechnology
Genetics
Bioengineering

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10.1109/BIBE.2007.4375585

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Khaladkar, M., Bellofatto, V., Wang, J. T. L., Patel, V., & Nakayama, M. K. (2007). Constrained RNA structural alignment: Algorithms and application to motif detection in the untranslated regions of Trypanosoma brucei mRNAs. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE (pp. 334-341). Article 4375585 (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE). https://doi.org/10.1109/BIBE.2007.4375585

Khaladkar, Mugdha ; Bellofatto, Vivian ; Wang, Jason T.L. et al. / Constrained RNA structural alignment : Algorithms and application to motif detection in the untranslated regions of Trypanosoma brucei mRNAs. Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. pp. 334-341 (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE).

@inproceedings{56813245e8894c03af6673e194a5f073,

title = "Constrained RNA structural alignment: Algorithms and application to motif detection in the untranslated regions of Trypanosoma brucei mRNAs",

abstract = "In this paper we propose a new method for aligning two RNA secondary structures by taking into account the presence of conserved RNA substructures, or constraints, in the alignment process. Our method allows the incorporation of specific knowledge about the RNA structures being analyzed while computing their alignment and thus is very useful for RNA motif detection. We develop statistical measures to assess the significance of alignment scores. Experimental results obtained by using the constrained alignment method to search for structural motifs in the untranslated regions of Trypanosoma brucei mRNAs demonstrate the good performance of the proposed method and its superiority over existing methods.",

author = "Mugdha Khaladkar and Vivian Bellofatto and Wang, {Jason T.L.} and Vandanaben Patel and Nakayama, {Marvin K.}",

year = "2007",

doi = "10.1109/BIBE.2007.4375585",

language = "English (US)",

isbn = "1424415098",

series = "Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE",

pages = "334--341",

booktitle = "Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE",

note = "7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE ; Conference date: 14-01-2007 Through 17-01-2007",

}

Khaladkar, M, Bellofatto, V, Wang, JTL, Patel, V & Nakayama, MK 2007, Constrained RNA structural alignment: Algorithms and application to motif detection in the untranslated regions of Trypanosoma brucei mRNAs. in Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE., 4375585, Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE, pp. 334-341, 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE, Boston, MA, United States, 1/14/07. https://doi.org/10.1109/BIBE.2007.4375585

Constrained RNA structural alignment: Algorithms and application to motif detection in the untranslated regions of Trypanosoma brucei mRNAs. / Khaladkar, Mugdha; Bellofatto, Vivian; Wang, Jason T.L. et al.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. p. 334-341 4375585 (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE).

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

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AB - In this paper we propose a new method for aligning two RNA secondary structures by taking into account the presence of conserved RNA substructures, or constraints, in the alignment process. Our method allows the incorporation of specific knowledge about the RNA structures being analyzed while computing their alignment and thus is very useful for RNA motif detection. We develop statistical measures to assess the significance of alignment scores. Experimental results obtained by using the constrained alignment method to search for structural motifs in the untranslated regions of Trypanosoma brucei mRNAs demonstrate the good performance of the proposed method and its superiority over existing methods.

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Khaladkar M, Bellofatto V, Wang JTL, Patel V, Nakayama MK. Constrained RNA structural alignment: Algorithms and application to motif detection in the untranslated regions of Trypanosoma brucei mRNAs. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. p. 334-341. 4375585. (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE). doi: 10.1109/BIBE.2007.4375585

Constrained RNA structural alignment: Algorithms and application to motif detection in the untranslated regions of Trypanosoma brucei mRNAs

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