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

Mugdha Khaladkar; Vivian Bellofatto; Jason Wang; Vandanaben Patel; Marvin 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 Wang, Vandanaben Patel, Marvin 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 - Dec 1 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

Access to Document

10.1109/BIBE.2007.4375585

Cite this

Khaladkar, M., Bellofatto, V., Wang, J., Patel, V., & Nakayama, M. (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 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 Jason Wang and Vandanaben Patel and Marvin Nakayama",

year = "2007",

month = dec,

day = "1",

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, J, Patel, V & Nakayama, M 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 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

TY - GEN

T1 - Constrained RNA structural alignment

T2 - 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

AU - Khaladkar, Mugdha

AU - Bellofatto, Vivian

AU - Wang, Jason

AU - Patel, Vandanaben

AU - Nakayama, Marvin

PY - 2007/12/1

Y1 - 2007/12/1

N2 - 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.

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.

UR - http://www.scopus.com/inward/record.url?scp=47649121789&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=47649121789&partnerID=8YFLogxK

U2 - 10.1109/BIBE.2007.4375585

DO - 10.1109/BIBE.2007.4375585

M3 - Conference contribution

AN - SCOPUS:47649121789

SN - 1424415098

SN - 9781424415090

T3 - Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

SP - 334

EP - 341

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

Y2 - 14 January 2007 through 17 January 2007

ER -

Khaladkar M, Bellofatto V, Wang J, Patel V, Nakayama M. 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

Abstract

Publication series

Other

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this