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

Research output: Chapter in Book/Report/Conference proceedingConference 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 languageEnglish (US)
Title of host publicationProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Pages334-341
Number of pages8
DOIs
StatePublished - Dec 1 2007
Event7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE - Boston, MA, United States
Duration: Jan 14 2007Jan 17 2007

Publication series

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

Other

Other7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
CountryUnited States
CityBoston, MA
Period1/14/071/17/07

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics
  • Bioengineering

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